Bioconductor Single Package Builder - Build History

Snapshot Date:

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

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	WARNINGS	OK	OK
nebbiolo2	Linux (Ubuntu 22.04.2 LTS)/x86_64	OK	WARNINGS	skipped	OK

lconway Summary

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Package: dreamlet

Version: 0.99.17

RVersion: 4.3

BiocVersion: 3.18

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

BuildTime: 4 minutes 24.06 seconds

CheckCommand: BiocCheckGitClone('dreamlet') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2955/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.install-out.txt dreamlet_0.99.17.tar.gz && BiocCheck('dreamlet_0.99.17.tar.gz', `new-package`=TRUE)

CheckTime: 7 minutes 22.04 seconds

BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh dreamlet_0.99.17.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir

BuildBinTime: 0 minutes 47.57 seconds

PackageFileSize: 3608.23 KiB

BuildID:: dreamlet_20230627145235

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: dreamlet. 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. Checking Package status: 0. Build Package status: 0.

lconway BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* preparing ‘dreamlet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: dreamlet
* saving partial Rd database
* 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 ‘dreamlet_0.99.17.tar.gz’

lconway CHECK output

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

 BiocCheckGitClone('dreamlet')

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

─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: dreamlet
─ PackageVersion: 0.99.17
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet
─ 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...
* 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/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.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 ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘0.99.17’
* 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 ‘dreamlet’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [34s/34s] OK
* checking Rd files ... [11s/11s] 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* 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 ... [172s/179s] OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
zenith_gsa-methods      55.314  6.320  68.832
sortCols-method          9.578  0.046   9.625
plotVarPart-methods      9.319  0.047   9.366
run_mash                 8.653  0.093   8.762
fitVarPart               8.294  0.037   8.333
plotPercentBars-methods  7.832  0.040   7.873
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [36s/51s]
 [37s/52s] 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 ... [10s/14s] OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.Rcheck/00check.log’
for details.






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

 BiocCheck('dreamlet_0.99.17.tar.gz')

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

─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: dreamlet
─ PackageVersion: 0.99.17
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd5cbcf022
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Microarray
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* Checking for library/require of dreamlet...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 18 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
    * WARNING: Empty or missing \value sections found in man pages.
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXwO6cI/file87cd1855cf07/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* 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; 405 lines (4%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 1905 lines (19%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 515 lines
      (5%) 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 | 1 WARNINGS | 9 NOTES

See the dreamlet.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 dreamlet_0.99.17.tar.gz'
>>>>>>> 

* installing *source* package ‘dreamlet’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/beachmat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/beachmat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c colsum_beachmat.cpp -o colsum_beachmat.o
In file included from colsum_beachmat.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -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 dreamlet.so RcppExports.o colsum_beachmat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/libdir/00LOCK-dreamlet/00new/dreamlet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (dreamlet)


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

>>>>>>> Paths before fix:
libdir/dreamlet/libs/dreamlet.so:
	dreamlet.so (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/dreamlet/libs/dreamlet.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/dreamlet/libs/dreamlet.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/dreamlet/libs/dreamlet.so"

>>>>>>> Paths after fix:

libdir/dreamlet/libs/dreamlet.so:
	dreamlet.so (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: dreamlet

Version: 0.99.17

RVersion: 4.3

BiocVersion: 3.18

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

BuildTime: 6 minutes 28.64 seconds

CheckCommand: BiocCheckGitClone('dreamlet') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2955/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.install-out.txt dreamlet_0.99.17.tar.gz && BiocCheck('dreamlet_0.99.17.tar.gz', `new-package`=TRUE)

CheckTime: 9 minutes 40.07 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 3460.21 KiB

BuildID:: dreamlet_20230627145235

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

nebbiolo2 BUILD SRC output

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

 R CMD BUILD

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

* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* preparing ‘dreamlet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: dreamlet
* saving partial Rd database
* 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 ‘dreamlet_0.99.17.tar.gz’

nebbiolo2 CHECK output

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

 BiocCheckGitClone('dreamlet')

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

─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: dreamlet
─ PackageVersion: 0.99.17
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet
─ 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...
* 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/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.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 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘0.99.17’
* 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 ‘dreamlet’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] 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 ... [48s/48s] OK
* checking Rd files ... [17s/18s] 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* 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 ... [221s/221s] OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
zenith_gsa-methods      59.385  2.136  61.522
fitVarPart              12.915  0.160  13.076
plotPercentBars-methods 12.268  0.048  12.316
sortCols-method         12.175  0.024  12.200
plotVarPart-methods     12.087  0.036  12.124
run_mash                10.777  0.044  10.824
aggregateNonCountSignal  5.102  0.305   5.406
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [40s/54s]
 [40s/54s] 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: 2 NOTEs
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.Rcheck/00check.log’
for details.






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

 BiocCheck('dreamlet_0.99.17.tar.gz')

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

─ BiocCheckVersion: 1.37.4
─ BiocVersion: 3.18
─ Package: dreamlet
─ PackageVersion: 0.99.17
─ sourceDir: /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet
─ installDir: /tmp/RtmpGEtlvY/file3860c578f2701a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/835eea423817c0b89b4f1389033fe77a827d5f52/dreamlet.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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Microarray
Search 'biocViews' at https://contributions.bioconductor.org
* 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...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* Checking for library/require of dreamlet...
* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 18 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
    * WARNING: Empty or missing \value sections found in man pages.
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /tmp/RtmpGEtlvY/file3860c5183e1af4/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* 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; 405 lines (4%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 1905 lines (19%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 515 lines
      (5%) 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 | 1 WARNINGS | 9 NOTES

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

nebbiolo2 BUILD BIN output

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