===============================
BiocCheckGitClone('scMET')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: scMET
─ PackageVersion: 0.99.11
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ 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/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scMET’ version ‘0.99.11’
* 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 ‘scMET’ can be installed ... [80s/81s] OK
* checking installed package size ... NOTE
installed size is 23.0Mb
sub-directories of 1Mb or more:
doc 3.0Mb
libs 18.6Mb
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [9s/9s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [91s/87s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scmet_plot_estimated_vs_true 16.419 0.076 15.706
scmet 13.588 0.293 13.136
scmet_plot_efdr_efnr_grid 12.044 0.040 11.317
scmet_plot_mean_var 11.965 0.075 11.307
scmet_plot_vf_tail_prob 11.972 0.040 11.440
scmet_hvf_lvf 11.728 0.088 11.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/2s] 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 ... OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET.Rcheck/00check.log’
for details.
===============================
BiocCheck('scMET_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: scMET
─ PackageVersion: 0.99.11
─ sourceDir: /tmp/Rtmp2DhkMT/fileeafeb41762600/scMET
─ installDir: /tmp/Rtmp2DhkMT/fileeafeb7ca23596
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 scMET...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 12
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.17% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* 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; 101 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1398 lines
(30%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 10 NOTES
See the scMET.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
BiocCheckGitClone('scMET')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: scMET
─ PackageVersion: 0.99.11
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ 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/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scMET’ version ‘0.99.11’
* 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 ‘scMET’ can be installed ... [175s/177s] OK
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
doc 3.4Mb
libs 2.0Mb
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [31s/31s] OK
* checking Rd files ... [1s/1s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [262s/263s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scmet_plot_estimated_vs_true 50.354 0.374 50.876
scmet 39.140 0.491 39.941
scmet_hvf_lvf 35.860 0.424 36.392
scmet_plot_vf_tail_prob 35.253 0.310 35.687
scmet_plot_efdr_efnr_grid 35.134 0.319 35.557
scmet_plot_mean_var 35.148 0.301 35.556
sce_to_scmet 10.988 0.403 11.639
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/7s]
[8s/8s] 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 ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET.Rcheck/00check.log’
for details.
===============================
BiocCheck('scMET_0.99.11.tar.gz')
===============================
─ BiocCheckVersion: 1.32.0
─ BiocVersion: 3.15
─ Package: scMET
─ PackageVersion: 0.99.11
─ sourceDir: /tmp/Rtmp7XOv6c/file113154c1fbc25/scMET
─ installDir: /tmp/Rtmp7XOv6c/file113157b71e075
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/scMET.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 scMET...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.There are 12
functions > 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
documentexported objects.
* NOTE: Usage of dontrun{} / donttest{} found in man page
examples.17% of man pages use one of these cases.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* 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; 101 lines (2%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1398 lines
(30%) are not.
See http://bioconductor.org/developers/how-to/coding-style/
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 | 10 NOTES
See the scMET.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir scMET_0.99.11.tar.gz'
>>>>>>>
* installing *source* package ‘scMET’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.2/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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -Wall -g -O2 -c stanExports_scmet.cc -o stanExports_scmet.o
In file included from stanExports_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.2/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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:283:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable]
int n = G.rows(); // number of states
^
In file included from stanExports_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion]
inline static double square(double x) { return square(x); }
^
In file included from stanExports_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:70:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable]
const size_t coupled_size = cvodes_data.coupled_ode_.size();
^
In file included from stanExports_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
static void set_zero_all_adjoints() {
^
In file included from stanExports_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:47:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static void set_zero_all_adjoints_nested() {
^
In file included from stanExports_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:278:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.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_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:328:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
using T_alpha_val = typename std::conditional_t<
^
In file included from stanExports_scmet.cc:5:
In file included from ./stanExports_scmet.h:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:51:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
using idx_t = typename index_type<matrix_v>::type;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
using idx_t = typename index_type<matrix_d>::type;
^
In file included from stanExports_scmet.cc:5:
./stanExports_scmet.h:403:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef]
typedef double local_scalar_t__;
^
28 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o scMET.so RcppExports.o stanExports_scmet.o -L/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2585/c13b0e35797be7c68c867e4042116f3f8e516be6/libdir/00LOCK-scMET/00new/scMET/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (scMET)
>>>>>>>
>>>>>>> FIXING LINKS FOR libdir/scMET/libs/scMET.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "libdir/scMET/libs/scMET.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "libdir/scMET/libs/scMET.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "libdir/scMET/libs/scMET.so"