Bioconductor Single Package Builder - Build History

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

 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
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
* 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_0.99.3.tar.gz’

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

 BiocCheckGitClone('dreamlet')

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

─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.3
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/8899dd18e59cad9c8d8b2f076cb4633a0b2a8cf7/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/2955/8899dd18e59cad9c8d8b2f076cb4633a0b2a8cf7/dreamlet.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘0.99.3’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
  Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2955/8899dd18e59cad9c8d8b2f076cb4633a0b2a8cf7/dreamlet.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] 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 ... [43s/43s] OK
* checking Rd files ... [12s/12s] WARNING
prepare_Rd: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
prepare_Rd: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
prepare_Rd: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
* 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 ... [189s/190s] OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
zenith_gsa-methods      57.749  3.728  62.011
fitVarPart              11.779  0.034  11.815
sortCols-method         11.628  0.041  11.670
plotVarPart-methods     11.394  0.033  11.428
plotPercentBars-methods 11.071  0.036  11.108
run_mash                 8.470  0.050   8.524
aggregateNonCountSignal  4.911  0.229   5.140
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [37s/55s]
 [37s/55s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [6s/15s] OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/2955/8899dd18e59cad9c8d8b2f076cb4633a0b2a8cf7/dreamlet.Rcheck/00check.log’
for details.






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

 BiocCheck('dreamlet_0.99.3.tar.gz')

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

─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.3
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d58d1be41
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/8899dd18e59cad9c8d8b2f076cb4633a0b2a8cf7/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...
    * NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* 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:
      Sequencing, Microarray, ImmunoOncology
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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(infile) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/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 19 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
  /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpWmSZ6l/filea00d2e68b25d/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; 392 lines (4%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 1922 lines (20%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 505 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 | 0 WARNINGS | 10 NOTES

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

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

 R CMD BUILD

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

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir dreamlet_0.99.3.tar.gz'
>>>>>>> 

* installing *source* package ‘dreamlet’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++11
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/beachmat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/beachmat/include' -I/usr/local/include    -fPIC  -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/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.3/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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++ -mmacosx-version-min=10.13 -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/usr/local/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/2955/8899dd18e59cad9c8d8b2f076cb4633a0b2a8cf7/libdir/00LOCK-dreamlet/00new/dreamlet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
in method for ‘dreamlet’ with signature ‘"dreamletProcessedData"’: no definition for class “dreamletProcessedData”
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
** testing if installed package keeps a record of temporary installation path
* DONE (dreamlet)


>>>>>>> 
>>>>>>> FIXING LINKS FOR libdir/dreamlet/libs/dreamlet.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libgcc_s.1.dylib" "libdir/dreamlet/libs/dreamlet.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3/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/Resources/lib/libquadmath.0.dylib" "libdir/dreamlet/libs/dreamlet.so"