[Bioc-devel] Issues with compiling edgeR 3.38.1 on macOS ARM
Leonardo Collado Torres
|co||@dotor @end|ng |rom gm@||@com
Tue Jun 7 22:54:47 CEST 2022
Hi Martin,
Awesome, thanks for the info!!! I had an older version installed. I had
installed what I thought were all the libraries, but gfortran was missing.
sudo R
source("https://mac.R-project.org/bin/install.R")
install.libs("all")
That's what I had used from
https://twitter.com/lcolladotor/status/1519665235652579328.
Here's the older version of gfortran I had (note the SDK soft link was
broken):
% ls -lh /opt/R/arm64/gfortran
total 0
lrwxr-xr-x 1 leocollado wheel 98 Dec 26 2020 SDK ->
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk
drwxr-xr-x 22 leocollado staff 704 Jan 1 2021 bin
drwxr-xr-x 3 leocollado staff 96 Dec 26 2020 include
drwxr-xr-x 41 leocollado staff 1.3K Jan 1 2021 lib
drwxr-xr-x 3 leocollado staff 96 Dec 26 2020 libexec
drwxr-xr-x 5 leocollado staff 160 Dec 26 2020 share
Rdeps %
% ls -lh
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk
gls: cannot access
'/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk':
No such file or directory
Here's the new version of gfortran (SDK soft link works):
% sudo tar fxz gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
% ls -lh /opt/R/arm64/gfortran/
total 0
lrwxr-xr-x 1 root admin 53 Mar 21 00:46 SDK ->
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk
drwxr-xr-x 32 root admin 1.0K Jun 7 16:45 bin
drwxr-xr-x 3 root admin 96 Mar 16 18:55 include
drwxr-xr-x 47 root admin 1.5K Jun 7 16:45 lib
drwxr-xr-x 3 root admin 96 Mar 16 18:55 libexec
drwxr-xr-x 7 root admin 224 Jun 7 16:45 share
% ls -lh /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk
lrwxr-xr-x 1 root wheel 14 May 24 17:47
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -> MacOSX11.3.sdk
% find /opt/R -name "libemutls*"
/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0/libemutls_w.a
/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1/libemutls_w.a
I also added this to my ~/.zshrc file:
export PATH=$PATH:/opt/R/arm64/gfortran/bin
Thank you again!
Leo
Successful installation log:
> BiocManager::install("edgeR")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
Installing package(s) 'edgeR'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2
:
cannot open URL '
https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2
:
cannot open URL '
https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2
:
cannot open URL '
https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2
:
cannot open URL '
https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
'
Warning: unable to access index for repository
https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2
:
cannot open URL '
https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
'
Package which is only available in source form, and may need
compilation of C/C++/Fortran: ‘edgeR’
Do you want to attempt to install these from sources? (Yes/no/cancel) y
installing the source package ‘edgeR’
trying URL '
https://bioconductor.org/packages/3.15/bioc/src/contrib/edgeR_3.38.1.tar.gz'
Content type 'application/x-gzip' length 1409283 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
* installing *source* package ‘edgeR’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_add_prior_count.cpp -o R_add_prior_count.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_ave_log_cpm.cpp -o R_ave_log_cpm.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_calculate_cpm.cpp -o R_calculate_cpm.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_check_poisson_bound.cpp -o R_check_poisson_bound.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_compute_apl.cpp -o R_compute_apl.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_compute_nbdev.cpp -o R_compute_nbdev.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_fit_levenberg.cpp -o R_fit_levenberg.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_fit_one_group.cpp -o R_fit_one_group.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_initialize_levenberg.cpp -o R_initialize_levenberg.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_loess_by_col.cpp -o R_loess_by_col.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_maximize_interpolant.cpp -o R_maximize_interpolant.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include"
-DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_process_hairpin_reads.c -o R_process_hairpin_reads.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
R_simple_good_turing.cpp -o R_simple_good_turing.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
add_prior.cpp -o add_prior.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
adj_coxreid.cpp -o adj_coxreid.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include"
-DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
fmm_spline.c -o fmm_spline.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
glm_levenberg.cpp -o glm_levenberg.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
glm_one_group.cpp -o glm_one_group.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
init.cpp -o init.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
interpolator.cpp -o interpolator.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
nbdev.cpp -o nbdev.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
objects.cpp -o objects.o
clang++ -arch arm64 -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/arm64/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o
R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o
R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o
R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o
R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o
add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o
init.o interpolator.o nbdev.o objects.o
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack
-L/Library/Frameworks/R.framework/Resources/lib -lRblas
-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
-L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-edgeR/00new/edgeR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation
path
* DONE (edgeR)
On Tue, Jun 7, 2022 at 3:46 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:
> Have you installed gfortran for Apple silicon Macs as described at
> https://mac.r-project.org/tools/ ? I have an older version installed
>
>
>
> $ find /opt/R -name "libemutls*"
>
>
> /opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0/libemutls_w.a
>
>
>
> But it seems like it is also in the more recent tarball
>
>
>
> $ tar tzf
> ~/Downloads/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz|grep libemutls
>
>
> opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1/libemutls_w.a
>
>
>
> *From: *Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
> Leonardo Collado Torres <lcolladotor using gmail.com>
> *Date: *Tuesday, June 7, 2022 at 3:23 PM
> *To: *Bioc-devel <bioc-devel using r-project.org>
> *Subject: *[Bioc-devel] Issues with compiling edgeR 3.38.1 on macOS ARM
>
> Hi Bioc-devel,
>
> I'm stumped with trying to install edgeR from Bioc 3.15 (release) on a
> macOS ARM computer.
>
> Has anyone encountered this error before?
>
> clang++ -arch arm64 -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/arm64/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o
> R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o
> R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o
> R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o
> R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o
> add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o
> init.o interpolator.o nbdev.o objects.o
> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
> -L/Library/Frameworks/R.framework/Resources/lib -lRblas
> -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
> -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> ld: warning: directory not found for option
> '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
> ld: library not found for -lemutls_w
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [edgeR.so] Error 1
> ERROR: compilation failed for package ‘edgeR’
>
> Best,
> Leo
>
>
> Full details:
>
>
> main > BiocManager::install("edgeR")
> 'getOption("repos")' replaces Bioconductor standard repositories, see
> '?repositories' for details
>
> replacement repositories:
> CRAN: https://cloud.r-project.org/
>
> Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
> Installing package(s) 'edgeR'
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
> '
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
> '
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
> '
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
> '
> Warning: unable to access index for repository
>
> https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2
> :
> cannot open URL '
>
> https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES
> '
> Package which is only available in source form, and may need compilation of
> C/C++/Fortran: ‘edgeR’
> Do you want to attempt to install these from sources? (Yes/no/cancel) y
> installing the source package ‘edgeR’
>
> trying URL '
>
> https://bioconductor.org/packages/3.15/bioc/src/contrib/edgeR_3.38.1.tar.gz'
> Content type 'application/x-gzip' length 1409283 bytes (1.3 MB)
> ==================================================
> downloaded 1.3 MB
>
> * installing *source* package ‘edgeR’ ...
> ** using staged installation
> ** libs
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_add_prior_count.cpp -o R_add_prior_count.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_ave_log_cpm.cpp -o R_ave_log_cpm.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_calculate_cpm.cpp -o R_calculate_cpm.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_check_poisson_bound.cpp -o R_check_poisson_bound.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_compute_apl.cpp -o R_compute_apl.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_compute_nbdev.cpp -o R_compute_nbdev.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_fit_levenberg.cpp -o R_fit_levenberg.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_fit_one_group.cpp -o R_fit_one_group.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_initialize_levenberg.cpp -o R_initialize_levenberg.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_loess_by_col.cpp -o R_loess_by_col.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_maximize_interpolant.cpp -o R_maximize_interpolant.o
> clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_process_hairpin_reads.c -o R_process_hairpin_reads.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> R_simple_good_turing.cpp -o R_simple_good_turing.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> add_prior.cpp -o add_prior.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> adj_coxreid.cpp -o adj_coxreid.o
> clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> fmm_spline.c -o fmm_spline.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> glm_levenberg.cpp -o glm_levenberg.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> glm_one_group.cpp -o glm_one_group.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> init.cpp -o init.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> interpolator.cpp -o interpolator.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> nbdev.cpp -o nbdev.o
> clang++ -arch arm64 -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
> -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
> objects.cpp -o objects.o
> clang++ -arch arm64 -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/arm64/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o
> R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o
> R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o
> R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o
> R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o
> add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o
> init.o interpolator.o nbdev.o objects.o
> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
> -L/Library/Frameworks/R.framework/Resources/lib -lRblas
> -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
> -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> ld: warning: directory not found for option
> '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
> ld: library not found for -lemutls_w
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [edgeR.so] Error 1
> ERROR: compilation failed for package ‘edgeR’
> * removing
>
> ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR’
> * restoring previous
>
> ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR’
>
> The downloaded source packages are in
>
> ‘/private/var/folders/9f/82m1lr2n1fv1mk91plf2l_dr0000gn/T/RtmpNJ5DDz/downloaded_packages’
> Old packages: 'BayesSpace', 'DESeq2', 'edgeR', 'genefilter',
> 'preprocessCore', 'scran', 'scuttle'
> Update all/some/none? [a/s/n]:
> n
> Warning message:
> In install.packages(...) :
> installation of package ‘edgeR’ had non-zero exit status
> main >
> Warning message:
> replacing previous import ‘utils::download.file’ by
> ‘restfulr::download.file’ when loading ‘rtracklayer’
> main >
> main >
> main > options(width = 120)
> main > sessioninfo::session_info()
> ─ Session info
>
> ───────────────────────────────────────────────────────────────────────────────────────────────────────
> setting value
> version R version 4.2.0 (2022-04-22)
> os macOS Monterey 12.4
> system aarch64, darwin20
> ui RStudio
> language (EN)
> collate en_US.UTF-8
> ctype en_US.UTF-8
> tz America/New_York
> date 2022-06-07
> rstudio 2022.02.3+492 Prairie Trillium (desktop)
> pandoc 2.17.1.1 @ /opt/homebrew/bin/pandoc
>
> ─ Packages
>
> ───────────────────────────────────────────────────────────────────────────────────────────────────────────
> package * version date (UTC) lib source
> AnnotationDbi 1.58.0 2022-04-26 [1] Bioconductor
> AnnotationHub 3.4.0 2022-04-26 [1] Bioconductor
> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
> attempt 0.3.1 2020-05-03 [1] CRAN (R 4.2.0)
> beachmat 2.12.0 2022-04-26 [1] Bioconductor
> beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.2.0)
> benchmarkme 1.0.7 2021-03-21 [1] CRAN (R 4.2.0)
> benchmarkmeData 1.0.4 2020-04-23 [1] CRAN (R 4.2.0)
> Biobase 2.56.0 2022-04-26 [1] Bioconductor
> BiocFileCache 2.4.0 2022-04-26 [1] Bioconductor
> BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
> BiocIO 1.6.0 2022-04-26 [1] Bioconductor
> BiocManager 1.30.18 2022-05-18 [1] CRAN (R 4.2.0)
> BiocNeighbors 1.14.0 2022-04-26 [1] Bioconductor
> BiocParallel 1.30.3 2022-06-05 [1] Bioconductor
> BiocSingular 1.12.0 2022-04-26 [1] Bioconductor
> BiocVersion 3.15.2 2022-03-29 [1] Bioconductor
> Biostrings 2.64.0 2022-04-26 [1] Bioconductor
> bit 4.0.4 2020-08-04 [1] CRAN (R 4.2.0)
> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
> blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
> brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0)
> bslib 0.3.1 2021-10-06 [1] CRAN (R 4.2.0)
> cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
> callr 3.7.0 2021-04-20 [1] CRAN (R 4.2.0)
> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0)
> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0)
> colorout 1.2-2 2022-03-01 [1] Github
> (jalvesaq/colorout using 79931fd)
> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
> config 0.3.1 2020-12-17 [1] CRAN (R 4.2.0)
> cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.2.0)
> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0)
> curl 4.3.2 2021-06-23 [1] CRAN (R 4.2.0)
> data.table 1.14.2 2021-09-27 [1] CRAN (R 4.2.0)
> DBI 1.1.2 2021-12-20 [1] CRAN (R 4.2.0)
> dbplyr 2.2.0 2022-06-05 [1] CRAN (R 4.2.0)
> DelayedArray 0.22.0 2022-04-26 [1] Bioconductor
> DelayedMatrixStats 1.18.0 2022-04-26 [1] Bioconductor
> desc 1.4.1 2022-03-06 [1] CRAN (R 4.2.0)
> devtools * 2.4.3 2021-11-30 [1] CRAN (R 4.2.0)
> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0)
> doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.2.0)
> dotCall64 1.0-1 2021-02-11 [1] CRAN (R 4.2.0)
> dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.0)
> dqrng 0.3.0 2021-05-01 [1] CRAN (R 4.2.0)
> DropletUtils 1.16.0 2022-04-26 [1] Bioconductor
> DT 0.23 2022-05-10 [1] CRAN (R 4.2.0)
> edgeR 3.37.1 2022-03-16 [1] Bioconductor
> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
> ExperimentHub 2.4.0 2022-04-26 [1] Bioconductor
> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
> fields 13.3 2021-10-30 [1] CRAN (R 4.2.0)
> filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0)
> foreach 1.5.2 2022-02-02 [1] CRAN (R 4.2.0)
> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
> generics 0.1.2 2022-01-31 [1] CRAN (R 4.2.0)
> GenomeInfoDb 1.32.2 2022-05-15 [1] Bioconductor
> GenomeInfoDbData 1.2.8 2022-04-28 [1] Bioconductor
> GenomicAlignments 1.32.0 2022-04-26 [1] Bioconductor
> GenomicRanges 1.48.0 2022-04-26 [1] Bioconductor
> ggbeeswarm 0.6.0 2017-08-07 [1] CRAN (R 4.2.0)
> ggplot2 3.3.6 2022-05-03 [1] CRAN (R 4.2.0)
> ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.2.0)
> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
> golem 0.3.2 2022-03-04 [1] CRAN (R 4.2.0)
> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0)
> gtable 0.3.0 2019-03-25 [1] CRAN (R 4.2.0)
> HDF5Array 1.24.1 2022-06-02 [1] Bioconductor
> hms 1.1.1 2021-09-26 [1] CRAN (R 4.2.0)
> htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.2.0)
> htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0)
> httpuv 1.6.5 2022-01-05 [1] CRAN (R 4.2.0)
> httr 1.4.3 2022-05-04 [1] CRAN (R 4.2.0)
> interactiveDisplayBase 1.34.0 2022-04-26 [1] Bioconductor
> IRanges 2.30.0 2022-04-26 [1] Bioconductor
> irlba 2.3.5 2021-12-06 [1] CRAN (R 4.2.0)
> iterators 1.0.14 2022-02-05 [1] CRAN (R 4.2.0)
> jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.2.0)
> jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0)
> KEGGREST 1.36.0 2022-04-26 [1] Bioconductor
> knitr 1.39 2022-04-26 [1] CRAN (R 4.2.0)
> later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0)
> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0)
> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.2.0)
> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0)
> limma 3.52.1 2022-05-15 [1] Bioconductor
> locfit 1.5-9.5 2022-03-03 [1] CRAN (R 4.2.0)
> lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.2.0)
> magick 2.7.3 2021-08-18 [1] CRAN (R 4.2.0)
> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
> maps 3.4.0 2021-09-25 [1] CRAN (R 4.2.0)
> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.0)
> MatrixGenerics 1.8.0 2022-04-26 [1] Bioconductor
> matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.0)
> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
> mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
> paletteer 1.4.0 2021-07-20 [1] CRAN (R 4.2.0)
> pillar 1.7.0 2022-02-01 [1] CRAN (R 4.2.0)
> pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.0)
> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
> pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.2.0)
> plotly 4.10.0 2021-10-09 [1] CRAN (R 4.2.0)
> png 0.1-7 2013-12-03 [1] CRAN (R 4.2.0)
> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
> processx 3.5.3 2022-03-25 [1] CRAN (R 4.2.0)
> promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
> prompt 1.0.1 2022-03-01 [1] Github
> (gaborcsardi/prompt using 7ef0f2e)
> ps 1.7.0 2022-04-23 [1] CRAN (R 4.2.0)
> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
> R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.2.0)
> R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.2.0)
> R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.2.0)
> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.2.0)
> RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
> Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.2.0)
> RCurl 1.98-1.6 2022-02-08 [1] CRAN (R 4.2.0)
> rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.2.0)
> remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
> restfulr 0.0.14 2022-06-05 [1] CRAN (R 4.2.0)
> rhdf5 2.40.0 2022-04-26 [1] Bioconductor
> rhdf5filters 1.8.0 2022-04-26 [1] Bioconductor
> Rhdf5lib 1.18.2 2022-05-15 [1] Bioconductor
> rjson 0.2.21 2022-01-09 [1] CRAN (R 4.2.0)
> rlang 1.0.2 2022-03-04 [1] CRAN (R 4.2.0)
> roxygen2 7.2.0 2022-05-13 [1] CRAN (R 4.2.0)
> rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
> Rsamtools 2.12.0 2022-04-26 [1] Bioconductor
> RSQLite 2.2.14 2022-05-07 [1] CRAN (R 4.2.0)
> rsthemes 0.3.1 2022-03-01 [1] Github
> (gadenbuie/rsthemes using bbe73ca)
> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0)
> rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.2.0)
> rtracklayer 1.56.0 2022-04-26 [1] Bioconductor
> S4Vectors 0.34.0 2022-04-26 [1] Bioconductor
> sass 0.4.1 2022-03-23 [1] CRAN (R 4.2.0)
> ScaledMatrix 1.4.0 2022-04-26 [1] Bioconductor
> scales 1.2.0 2022-04-13 [1] CRAN (R 4.2.0)
> scater 1.24.0 2022-04-26 [1] Bioconductor
> scuttle 1.5.1 2022-03-15 [1] Bioconductor
> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
> shiny 1.7.1 2021-10-02 [1] CRAN (R 4.2.0)
> shinyWidgets 0.7.0 2022-05-11 [1] CRAN (R 4.2.0)
> SingleCellExperiment 1.18.0 2022-04-26 [1] Bioconductor
> spam 2.8-0 2022-01-06 [1] CRAN (R 4.2.0)
> sparseMatrixStats 1.8.0 2022-04-26 [1] Bioconductor
> SpatialExperiment 1.6.0 2022-04-26 [1] Bioconductor
> spatialLIBD 1.9.3 2022-05-27 [1] Github
> (LieberInstitute/spatialLIBD using 32c3a41)
> stringi 1.7.6 2021-11-29 [1] CRAN (R 4.2.0)
> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0)
> SummarizedExperiment 1.26.1 2022-04-29 [1] Bioconductor
> suncalc 0.5.0 2019-04-03 [1] CRAN (R 4.2.0)
> testthat * 3.1.4 2022-04-26 [1] CRAN (R 4.2.0)
> tibble 3.1.7 2022-05-03 [1] CRAN (R 4.2.0)
> tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.2.0)
> tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0)
> usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0)
> vipor 0.4.5 2017-03-22 [1] CRAN (R 4.2.0)
> viridis 0.6.2 2021-10-13 [1] CRAN (R 4.2.0)
> viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.2.0)
> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
> xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0)
> XML 3.99-0.9 2022-02-24 [1] CRAN (R 4.2.0)
> xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
> XVector 0.36.0 2022-04-26 [1] Bioconductor
> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
> zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
>
> [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
>
>
> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
>
> Leonardo Collado Torres, Ph. D.
> Investigator
>
> LIEBER INSTITUTE *for* BRAIN DEVELOPMENT
> 855 N. Wolfe St., Suite 300
> Baltimore, MD 21205
> lcolladotor.github.io
> lcolladotor using gmail.com
>
> [[alternative HTML version deleted]]
>
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