[Bioc-devel] Issues with compiling edgeR 3.38.1 on macOS ARM
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Tue Jun 7 21:46:50 CEST 2022
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
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