===============================
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 ‘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_0.99.4.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘dreamlet/vignettes/cell_level_covariates_cache/html/aggr_means_cbc9b3e873167f53c5e4130672f2b9c6.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘dreamlet/vignettes/cell_level_covariates_cache/html/preprocess.data_9ef0ac71ea95e1c9a03d03db9e058dda.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘dreamlet/vignettes/cell_level_covariates_cache/html/preprocess.data_9ef0ac71ea95e1c9a03d03db9e058dda.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘dreamlet/vignettes/cell_level_covariates_cache/html/preprocess.data_9ef0ac71ea95e1c9a03d03db9e058dda.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘dreamlet/vignettes/cell_level_covariates_cache/html/processAssays_0313b37f09922368f66daa86ee5861ec.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘dreamlet/vignettes/cell_level_covariates_cache/html/processAssays_0313b37f09922368f66daa86ee5861ec.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘dreamlet/vignettes/cell_level_covariates_cache/html/processAssays_0313b37f09922368f66daa86ee5861ec.rdx’
===============================
BiocCheckGitClone('dreamlet')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.4
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/60663517aff48b893177a76428aca78afbcfe4cb/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/2955/60663517aff48b893177a76428aca78afbcfe4cb/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 ‘0.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
dreamlet/vignettes/cell_level_covariates_cache/html/aggr_means_cbc9b3e873167f53c5e4130672f2b9c6.RData
dreamlet/vignettes/cell_level_covariates_cache/html/preprocess.data_9ef0ac71ea95e1c9a03d03db9e058dda.RData
dreamlet/vignettes/cell_level_covariates_cache/html/preprocess.data_9ef0ac71ea95e1c9a03d03db9e058dda.rdb
dreamlet/vignettes/cell_level_covariates_cache/html/preprocess.data_9ef0ac71ea95e1c9a03d03db9e058dda.rdx
dreamlet/vignettes/cell_level_covariates_cache/html/processAssays_0313b37f09922368f66daa86ee5861ec.RData
dreamlet/vignettes/cell_level_covariates_cache/html/processAssays_0313b37f09922368f66daa86ee5861ec.rdb
dreamlet/vignettes/cell_level_covariates_cache/html/processAssays_0313b37f09922368f66daa86ee5861ec.rdx
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dreamlet’ can be installed ... OK
* 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 ... [13s/13s] 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 ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] 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 ... [45s/45s] OK
* checking Rd files ... [13s/13s] WARNING
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 ... [195s/196s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
zenith_gsa-methods 60.184 3.217 63.743
sortCols-method 12.509 0.026 12.536
fitVarPart 12.302 0.040 12.344
plotVarPart-methods 11.932 0.022 11.955
plotPercentBars-methods 11.512 0.022 11.534
run_mash 8.813 0.035 8.850
aggregateNonCountSignal 5.069 0.243 5.312
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [38s/55s]
[38s/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 ... [7s/7s] OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2955/60663517aff48b893177a76428aca78afbcfe4cb/dreamlet.Rcheck/00check.log’
for details.
===============================
BiocCheck('dreamlet_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.35.15
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.4
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb599d0d8f
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2955/60663517aff48b893177a76428aca78afbcfe4cb/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...
* ERROR: Package tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
* WARNING: Package files exceed the 5MB size limit.
* 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...
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
* 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//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/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//RtmpXTD4nb/filed1eb72756029/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/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/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//RtmpXTD4nb/filed1eb72756029/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//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/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//RtmpXTD4nb/filed1eb72756029/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//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpXTD4nb/filed1eb72756029/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//RtmpXTD4nb/filed1eb72756029/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; 1846 lines (19%) 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 ──
1 ERRORS | 1 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_0.99.4.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/2955/60663517aff48b893177a76428aca78afbcfe4cb/libdir/00LOCK-dreamlet/00new/dreamlet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
** 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 ‘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 ‘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"