[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 at 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 at 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 at 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 at 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 at gmail.com