Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/decontX

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
lconway	macOS 12.6.5 Monterey/x86_64	OK	OK	OK	OK
nebbiolo2	Linux (Ubuntu 22.04.2 LTS)/x86_64	OK	OK	skipped	OK

lconway Summary

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Package: decontX

Version: 0.99.4

RVersion: 4.3

BiocVersion: 3.18

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data decontX

BuildTime: 7 minutes 4.37 seconds

CheckCommand: BiocCheckGitClone('decontX') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3020/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.install-out.txt decontX_0.99.4.tar.gz && BiocCheck('decontX_0.99.4.tar.gz', `new-package`=TRUE)

CheckTime: 6 minutes 48.53 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh decontX_0.99.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 2 minutes 4.95 seconds

PackageFileSize: 2066.76 KiB

BuildID:: decontX_20231017025138

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: decontX. Starting Build package. Starting Check package. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0.

lconway BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘decontX/DESCRIPTION’ ... OK
* preparing ‘decontX’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘decontX_0.99.4.tar.gz’

lconway CHECK output

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===============================

 BiocCheckGitClone('decontX')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: decontX
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decontX/DESCRIPTION’ ... OK
* this is package ‘decontX’ version ‘0.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decontX’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [43s/43s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/74s] OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
decontPro                   12.420  0.365  12.802
decontX                     11.749  0.530  12.284
plotDecontXMarkerPercentage  9.353  0.113   9.469
plotDecontXMarkerExpression  8.360  0.091   8.455
plotDecontXContamination     7.798  0.079   7.881
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [66s/67s]
 [66s/67s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [6s/7s] OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.Rcheck/00check.log’
for details.






===============================

 BiocCheck('decontX_0.99.4.tar.gz')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: decontX
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp5BNSpx/fileb623467b20d/decontX
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp5BNSpx/fileb621b83bfe
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of decontX...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 15 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 54 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1119 lines
      (27%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 8 NOTES

See the decontX.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

lconway BUILD BIN output

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===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir decontX_0.99.4.tar.gz'
>>>>>>> 

* installing *source* package ‘decontX’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c DecontX.cpp -o DecontX.o
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
DecontX.cpp:321:10: warning: variable 'x' set but not used [-Wunused-but-set-variable]
  double x;
         ^
19 warnings generated.


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
18 warnings generated.


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c matrixNorm.cpp -o matrixNorm.o


clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matrixSums.c -o matrixSums.o


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c matrixSumsSparse.cpp -o matrixSumsSparse.o
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
18 warnings generated.


clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c stanExports_shrinkage.cc -o stanExports_shrinkage.o
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/err.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor_corr.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/err/check_unit_vector.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/abs.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/hypot.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/apply_scalar_binary.hpp:9:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:33:8: warning: unused variable 'error' [-Wunused-variable]
  bool error = false;
       ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/err.hpp:50:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/err/hmm_check.hpp:33:7: warning: unused variable 'n_transitions' [-Wunused-variable]
  int n_transitions = log_omegas.cols() - 1;
      ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:118:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/gp_matern52_cov.hpp:275:10: warning: unused variable 'neg_root_5' [-Wunused-variable]
  double neg_root_5 = -root_5;
         ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:183:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/log_mix.hpp:86:13: warning: unused variable 'N' [-Wunused-variable]
  const int N = stan::math::size(theta);
            ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:87:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/double_exponential_cdf.hpp:82:10: warning: unused variable 'N' [-Wunused-variable]
  size_t N = max_size(y, mu, sigma);
         ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:128:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/gaussian_dlm_obs_rng.hpp:98:7: warning: unused variable 'n' [-Wunused-variable]
  int n = G.rows();  // number of states
      ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:139:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/hmm_marginal.hpp:26:13: warning: unused variable 'n_states' [-Wunused-variable]
  const int n_states = omegas.rows();
            ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:315:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/std_normal_rng.hpp:23:22: warning: unused variable 'function' [-Wunused-variable]
  static const char* function = "std_normal_rng";
                     ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:335:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/von_mises_cdf.hpp:72:10: warning: unused variable 'ck' [-Wunused-variable]
  double ck = 50;
         ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/indexing.hpp:9:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:610:13: warning: unused variable 'cols' [-Wunused-variable]
  const int cols = rvalue_index_size(idxs.tail_.head_, x_ref.cols());
            ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/indexing.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:241:22: warning: unused variable 'x_cols' [-Wunused-variable]
  const Eigen::Index x_cols = x.cols();
                     ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_division.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_multiplication.hpp:7:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_subtraction.hpp:88:43: warning: lambda capture 'b' is not used [-Wunused-lambda-capture]
                            [avi = a.vi_, b](const auto& vi) mutable {
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_minus_equal.hpp:24:16: note: in instantiation of function template specialization 'stan::math::operator-<double, nullptr>' requested here
  vi_ = (*this - b).vi_;
               ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/core/complex_base.hpp:136:9: note: in instantiation of member function 'stan::math::var_value<double>::operator-=' requested here
    re_ -= x;
        ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/core/operator_subtraction.hpp:24:5: note: in instantiation of function template specialization 'stan::math::complex_base<stan::math::var_value<double>>::operator-=<int>' requested here
  y -= rhs;
    ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/core/operator_subtraction.hpp:55:20: note: in instantiation of function template specialization 'stan::math::internal::complex_subtract<std::complex<stan::math::var>, int>' requested here
  return internal::complex_subtract(x, y);
                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/acosh.hpp:105:31: note: in instantiation of function template specialization 'stan::math::operator-<stan::math::var_value<double>, int>' requested here
  auto y = log(z + sqrt(z * z - 1));
                              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun/acosh.hpp:94:32: note: in instantiation of function template specialization 'stan::math::internal::complex_acosh<stan::math::var_value<double>>' requested here
  return stan::math::internal::complex_acosh(z);
                               ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:28:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_addition.hpp:84:43: warning: lambda capture 'b' is not used [-Wunused-lambda-capture]
                            [avi = a.vi_, b](const auto& vi) mutable {
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun/grad_inc_beta.hpp:45:43: note: in instantiation of function template specialization 'stan::math::operator+<int, nullptr>' requested here
    grad_2F1(dF1, dF2, a + b, var(1.0), a + 1, z);
                                          ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:28:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_addition.hpp:84:43: warning: lambda capture 'b' is not used [-Wunused-lambda-capture]
                            [avi = a.vi_, b](const auto& vi) mutable {
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/trigamma.hpp:63:31: note: in instantiation of function template specialization 'stan::math::operator+<double, nullptr>' requested here
    value = -trigamma_impl(-x + 1.0) + square(pi() / sin(-pi() * x));
                              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun/trigamma.hpp:23:44: note: in instantiation of function template specialization 'stan::math::trigamma_impl<stan::math::var_value<double>>' requested here
inline var trigamma(const var& u) { return trigamma_impl(u); }
                                           ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_division.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_multiplication.hpp:7:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_subtraction.hpp:113:43: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
                            [bvi = b.vi_, a](const auto& vi) mutable {
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/lub_constrain.hpp:115:24: note: in instantiation of function template specialization 'stan::math::operator-<double, nullptr>' requested here
    lp += log(ub - lb) - x - 2 * log1p(exp_minus_x);
                       ^
./stanExports_shrinkage.h:404:27: note: in instantiation of function template specialization 'stan::math::lub_constrain<stan::math::var_value<double>, int, double, stan::math::var_value<double>>' requested here
              stan::math::lub_constrain(
                          ^
./stanExports_shrinkage.h:1106:14: note: in instantiation of function template specialization 'model_shrinkage_namespace::model_shrinkage::log_prob_impl<true, true, std::vector<stan::math::var_value<double>>, std::vector<int>, nullptr, nullptr>' requested here
      return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_shrinkage_namespace::model_shrinkage::log_prob<true, true, stan::math::var_value<double>>' requested here
    var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
                                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:166:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_shrinkage_namespace::model_shrinkage>' requested here
      log_prob = stan::model::log_prob_grad<true, Jacobian>(
                              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
  std::vector<double> cont_vector = util::initialize(
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_shrinkage_namespace::model_shrinkage>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
    ret = command(args, model_, holder, names_oi_tidx_,
          ^
stanExports_shrinkage.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
    .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
                                                                                      ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:52:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/precomputed_gradients.hpp:83:59: warning: lambda capture 'this' is not used [-Wunused-lambda-capture]
        container_operands_(index_apply<N_containers>([&, this](auto... Is) {
                                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/functor/operands_and_partials.hpp:167:16: note: in instantiation of function template specialization 'stan::math::precomputed_gradients_vari_template<>::precomputed_gradients_vari_template<>' requested here
    return new precomputed_gradients_vari_template<
               ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:113:23: note: in instantiation of member function 'stan::math::operands_and_partials<const stan::math::var_value<double> &, const int &, const double &, double, double, stan::math::var_value<double>>::build' requested here
  return ops_partials.build(logp);
                      ^
./stanExports_shrinkage.h:515:24: note: in instantiation of function template specialization 'stan::math::normal_lpdf<true, stan::math::var_value<double>, int, double, nullptr>' requested here
        lp_accum__.add(normal_lpdf<propto__>(tau_a, 0, delta_sd));
                       ^
./stanExports_shrinkage.h:1106:14: note: in instantiation of function template specialization 'model_shrinkage_namespace::model_shrinkage::log_prob_impl<true, true, std::vector<stan::math::var_value<double>>, std::vector<int>, nullptr, nullptr>' requested here
      return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_shrinkage_namespace::model_shrinkage::log_prob<true, true, stan::math::var_value<double>>' requested here
    var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
                                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:166:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_shrinkage_namespace::model_shrinkage>' requested here
      log_prob = stan::model::log_prob_grad<true, Jacobian>(
                              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
  std::vector<double> cont_vector = util::initialize(
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_shrinkage_namespace::model_shrinkage>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
    ret = command(args, model_, holder, names_oi_tidx_,
          ^
stanExports_shrinkage.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
    .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
                                                                                      ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:52:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/precomputed_gradients.hpp:86:60: warning: lambda capture 'this' is not used [-Wunused-lambda-capture]
        container_gradients_(index_apply<N_containers>([&, this](auto... Is) {
                                                           ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_division.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_multiplication.hpp:7:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_subtraction.hpp:113:43: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
                            [bvi = b.vi_, a](const auto& vi) mutable {
                                          ^
./stanExports_shrinkage.h:539:41: note: in instantiation of function template specialization 'stan::math::operator-<int, nullptr>' requested here
                  (((((OC[(m - 1)] * (1 - background[(n - 1)][(m - 1)])) *
                                        ^
./stanExports_shrinkage.h:1106:14: note: in instantiation of function template specialization 'model_shrinkage_namespace::model_shrinkage::log_prob_impl<true, true, std::vector<stan::math::var_value<double>>, std::vector<int>, nullptr, nullptr>' requested here
      return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_shrinkage_namespace::model_shrinkage::log_prob<true, true, stan::math::var_value<double>>' requested here
    var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
                                   ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:166:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_shrinkage_namespace::model_shrinkage>' requested here
      log_prob = stan::model::log_prob_grad<true, Jacobian>(
                              ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
  std::vector<double> cont_vector = util::initialize(
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_shrinkage_namespace::model_shrinkage>' requested here
    return_code = stan::services::diagnose::diagnose(model,
                                            ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
    ret = command(args, model_, holder, names_oi_tidx_,
          ^
stanExports_shrinkage.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_shrinkage_namespace::model_shrinkage, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
    .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
                                                                                      ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:48:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_base.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:59:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'static' function 'set_zero_all_adjoints' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static void set_zero_all_adjoints() {
            ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:110:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp:34:9: warning: unused type alias 'value_t' [-Wunused-local-typedef]
  using value_t = value_type_t<EigMat>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:319:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/tail.hpp:46:9: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
  using idx_t = index_type_t<std::vector<T>>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp:59:9: warning: unused type alias 'T_y_val' [-Wunused-local-typedef]
  using T_y_val =
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp:50:9: warning: unused type alias 'T_partials_matrix' [-Wunused-local-typedef]
  using T_partials_matrix = Eigen::Matrix<T_partials_return, Eigen::Dynamic, 1>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_proportion_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp:55:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
  using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:63:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/cauchy_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp:45:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
  using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:74:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/dirichlet_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef]
  using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:91:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/double_exponential_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:44:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
  using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:111:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp:30:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
  using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:245:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp:76:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
  using T_partials_array = Eigen::Array<T_partials_return, -1, 1>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:277:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp:62:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
  using T_alpha_val = typename std::conditional_t<
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:49:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:32:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp:83:11: warning: unused type alias 'Block_' [-Wunused-local-typedef]
    using Block_ = Eigen::Block<Eigen::MatrixXd>;
          ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:49:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:34:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp:32:9: warning: unused type alias 'T_scalar' [-Wunused-local-typedef]
  using T_scalar = value_type_t<T>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:49:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:71:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp:64:9: warning: unused type alias 'value_t' [-Wunused-local-typedef]
  using value_t = value_type_t<VarMat>;
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/indexing.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp:349:9: warning: unused type alias 'pair_type' [-Wunused-local-typedef]
  using pair_type = std::pair<int, arena_vec>;
        ^
53 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o decontX.so DecontX.o RcppExports.o matrixNorm.o matrixSums.o matrixSumsSparse.o stanExports_shrinkage.o -L/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/libdir/00LOCK-decontX/00new/decontX/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (decontX)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR libdir/decontX/libs/decontX.so
>>>>>>> 

>>>>>>> Paths before fix:
libdir/decontX/libs/decontX.so:
	decontX.so (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "libdir/decontX/libs/decontX.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "libdir/decontX/libs/decontX.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "libdir/decontX/libs/decontX.so"

>>>>>>> Paths after fix:
libdir/decontX/libs/decontX.so:
	decontX.so (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

nebbiolo2 Summary

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Package: decontX

Version: 0.99.4

RVersion: 4.3

BiocVersion: 3.18

BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data decontX

BuildTime: 8 minutes 6.58 seconds

CheckCommand: BiocCheckGitClone('decontX') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3020/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.install-out.txt decontX_0.99.4.tar.gz && BiocCheck('decontX_0.99.4.tar.gz', `new-package`=TRUE)

CheckTime: 6 minutes 46.22 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 1724.31 KiB

BuildID:: decontX_20231017025138

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: decontX. Starting Build package. Starting Check package.

nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘decontX/DESCRIPTION’ ... OK
* preparing ‘decontX’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘decontX_0.99.4.tar.gz’

nebbiolo2 CHECK output

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===============================

 BiocCheckGitClone('decontX')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: decontX
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decontX/DESCRIPTION’ ... OK
* this is package ‘decontX’ version ‘0.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decontX’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 45.7Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [13s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/12s] OK
* checking loading without being on the library search path ... [16s/16s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [42s/41s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [74s/74s] OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
decontPro                   11.337  0.299  11.640
decontX                     10.422  0.315  10.738
plotDecontXMarkerExpression  8.934  0.140   9.074
plotDecontXContamination     8.746  0.125   8.869
plotDecontXMarkerPercentage  8.699  0.108   8.808
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [70s/70s]
 [70s/70s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE

Status: 3 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.Rcheck/00check.log’
for details.






===============================

 BiocCheck('decontX_0.99.4.tar.gz')

===============================

─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: decontX
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmpVTNsS4/file21d8355509458/decontX
─ installDir: /tmp/RtmpVTNsS4/file21d83532471f60
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3020/ca82730d8a9715c04526d1919a1f98c5c02ff20f/decontX.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of decontX...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 15 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 54 lines (1%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 1119 lines
      (27%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 8 NOTES

See the decontX.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

nebbiolo2 BUILD BIN output

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