> R.version
_
platform aarch64-apple-darwin20
arch aarch64
os darwin20
system aarch64, darwin20
status
major 4
minor 4.0
year 2024
month 04
day 24
svn rev 86474
language R
version.string R version 4.4.0 (2024-04-24)
nickname Puppy Cup
I had installed Seurat 5.1.0.and SeuratData 0.2.2.9001
Then I tried to install Azimuth using remotes:
> remotes::install_github("satijalab/azimuth", ref = "master")
Downloading GitHub repo satijalab/azimuth@master
Installing 3 packages: DirichletMultinomial, TFBSTools, glmGamPoi
Installing packages into ‘/Users/319801/Library/R/arm64/4.4/library’
(as ‘lib’ is unspecified)
Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES': HTTP status was '404 Not Found'Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES': HTTP status was '404 Not Found'Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES': HTTP status was '404 Not Found'Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 248Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES': HTTP status was '404 Not Found'Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'Warning: downloaded length 0 != reported length 11310Warning: cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11310Warning: cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11310Warning: cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES': HTTP status was '404 Not Found'Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'Packages which are only available in source form, and may need compilation of C/C++/Fortran:
‘DirichletMultinomial’ ‘TFBSTools’ ‘glmGamPoi’
Do you want to attempt to install these from sources? (Yes/no/cancel) y
installing the source packages ‘DirichletMultinomial’, ‘TFBSTools’, ‘glmGamPoi’
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DirichletMultinomial_1.44.0.tar.gz'
Content type 'application/gzip' length 438123 bytes (427 KB)
==================================================
downloaded 427 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/TFBSTools_1.40.0.tar.gz'
Content type 'application/gzip' length 587109 bytes (573 KB)
==================================================
downloaded 573 KB
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/glmGamPoi_1.14.3.tar.gz'
Content type 'application/gzip' length 2104554 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
* installing *source* package ‘DirichletMultinomial’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX13.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_DirichletMultinomial.c -o R_init_DirichletMultinomial.o
/bin/sh: gsl-config: command not found
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -falign-functions=64 -Wall -g -O2 -c dirichlet_fit.c -o dirichlet_fit.o
/bin/sh: gsl-config: command not found
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC -falign-functions=64 -Wall -g -O2 -c dirichlet_fit_main.c -o dirichlet_fit_main.o
/bin/sh: gsl-config: command not found
dirichlet_fit_main.c:1:10: fatal error: 'gsl/gsl_rng.h' file not found
#include <gsl/gsl_rng.h>
^~~~~~~~~~~~~~~
1 error generated.
make: *** [dirichlet_fit_main.o] Error 1
ERROR: compilation failed for package ‘DirichletMultinomial’
* removing ‘/Users/319801/Library/R/arm64/4.4/library/DirichletMultinomial’
Warning: installation of package ‘DirichletMultinomial’ had non-zero exit status* installing *source* package ‘glmGamPoi’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX13.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/319801/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/319801/Library/R/arm64/4.4/library/RcppArmadillo/include' -I'/Users/319801/Library/R/arm64/4.4/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/319801/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/319801/Library/R/arm64/4.4/library/RcppArmadillo/include' -I'/Users/319801/Library/R/arm64/4.4/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c beta_estimation.cpp -o beta_estimation.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/319801/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/319801/Library/R/arm64/4.4/library/RcppArmadillo/include' -I'/Users/319801/Library/R/arm64/4.4/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c deviance.cpp -o deviance.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/319801/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/319801/Library/R/arm64/4.4/library/RcppArmadillo/include' -I'/Users/319801/Library/R/arm64/4.4/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c overdispersion.cpp -o overdispersion.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Users/319801/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/319801/Library/R/arm64/4.4/library/RcppArmadillo/include' -I'/Users/319801/Library/R/arm64/4.4/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/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/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0'
ld: warning: directory not found for option '-L/opt/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [glmGamPoi.so] Error 1
ERROR: compilation failed for package ‘glmGamPoi’
* removing ‘/Users/319801/Library/R/arm64/4.4/library/glmGamPoi’
Warning: installation of package ‘glmGamPoi’ had non-zero exit statusERROR: dependency ‘DirichletMultinomial’ is not available for package ‘TFBSTools’
* removing ‘/Users/319801/Library/R/arm64/4.4/library/TFBSTools’
Warning: installation of package ‘TFBSTools’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/jn/8fvwzmmj2vgcrh1lgmrjrycc6n1vgl/T/RtmpbPfHtO/downloaded_packages’
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/jn/8fvwzmmj2vgcrh1lgmrjrycc6n1vgl/T/RtmpbPfHtO/remotesa26814d46194/satijalab-azimuth-243ee5d/DESCRIPTION’ ...
─ preparing ‘Azimuth’:
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘Azimuth_0.5.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
Installing package into ‘/Users/319801/Library/R/arm64/4.4/library’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘glmGamPoi’, ‘TFBSTools’ are not available for package ‘Azimuth’
* removing ‘/Users/319801/Library/R/arm64/4.4/library/Azimuth’
Warning: installation of package ‘/var/folders/jn/8fvwzmmj2vgcrh1lgmrjrycc6n1vgl/T//RtmpbPfHtO/filea2684917a8b0/Azimuth_0.5.0.tar.gz’ had non-zero exit status
I also tried devtools::install_github("satijalab/azimuth", "seurat5") but the result is the same, it is telling me glmGamPoi and TFBSTools are not available. I also had the error ERROR: compilation failed for package ‘DirichletMultinomial’ which I do not how to address.
R Version
I had installed Seurat 5.1.0.and SeuratData 0.2.2.9001
Then I tried to install Azimuth using remotes:
I also tried devtools::install_github("satijalab/azimuth", "seurat5") but the result is the same, it is telling me glmGamPoi and TFBSTools are not available. I also had the error ERROR: compilation failed for package ‘DirichletMultinomial’ which I do not how to address.
I hope you can help me and thank you!
Where I can find this two dependencies?