Hello I'am unable to install Azimuth locally on R.

remotes::install_github('satijalab/azimuth', ref = 'master')

Downloading GitHub repo satijalab/azimuth@master These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: HDF5Array (1.30.0 -> 1.30.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 HDF5Array (1.30.0 -> 1.30.1) [CRAN] glmGamPoi (NA -> 1.14.3) [CRAN] Installing 2 packages: HDF5Array, glmGamPoi

There is a binary version available but the source version is later: binary source needs_compilation HDF5Array 1.30.0 1.30.1 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes Package which is only available in source form, and may need compilation of C/C++/Fortran: 'glmGamPoi' Do you want to attempt to install these from sources? (Yes/no/cancel) Yes installing the source packages 'HDF5Array', 'glmGamPoi'

x-gzip' length 8098441 bytes (7.7 MB)

downloaded 7.7 MB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/glmGamPoi_1.14.3.tar.gz' Content type 'application/x-gzip' length 2104554 bytes (2.0 MB)

downloaded 2.0 MB

installing source package ‘HDF5Array’ ... using staged installation libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX14.2.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c H5File.c -o H5File.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c global_errmsg_buf.c -o global_errmsg_buf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5dimscales.c -o h5dimscales.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c uaselection.c -o uaselection.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_helpers.c -o h5mread_helpers.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_startscounts.c -o h5mread_startscounts.o h5mread_startscounts.c:300:16: warning: variable 'num_hyperslabs' set but not used [-Wunused-but-set-variable] long long int num_hyperslabs; ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChunkIterator.c -o ChunkIterator.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_index.c -o h5mread_index.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_sparse.c -o h5mread_sparse.o h5mread_sparse.c:123:13: warning: unused function 'NOT_USED_make_nzindex_from_buf' [-Wunused-function] static SEXP NOT_USED_make_nzindex_from_buf(const IntAE nzindex_buf, ^ h5mread_sparse.c:179:13: warning: unused function 'NOT_USED_make_nzdata_from_IntAE_bufs' [-Wunused-function] static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE nzdata_bufs, ^ h5mread_sparse.c:206:13: warning: unused function 'NOT_USED_make_nzindex_from_bufs' [-Wunused-function] static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs, ^ 3 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread.c -o h5mread.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5summarize.c -o h5summarize.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_HDF5Array.c -o R_init_HDF5Array.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_hl.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: library 'crypto' not found clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [HDF5Array.so] Error 1 ERROR: compilation failed for package ‘HDF5Array’
removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/HDF5Array’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/HDF5Array’
installing source package ‘glmGamPoi’ ... using staged installation libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX14.2.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c beta_estimation.cpp -o beta_estimation.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c deviance.cpp -o deviance.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c overdispersion.cpp -o overdispersion.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: search path '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0' not found ld: warning: search path '/opt/gfortran/lib' not found ld: library 'gfortran' not found 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 ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/glmGamPoi’

The downloaded source packages are in '/private/var/folders/v5/618fyvl92kldww407cwy53fr0000gq/T/Rtmpoq9gaz/downloaded_packages' ── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/v5/618fyvl92kldww407cwy53fr0000gq/T/Rtmpoq9gaz/remotes17f19c1acaf4/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’

ERROR: dependency ‘glmGamPoi’ is not available for package ‘Azimuth’

removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Azimuth’ Warning messages: 1: In i.p(...) : installation of package 'HDF5Array' had non-zero exit status 2: In i.p(...) : installation of package 'glmGamPoi' had non-zero exit status 3: In i.p(...) : installation of package '/var/folders/v5/618fyvl92kldww407cwy53fr0000gq/T//Rtmpoq9gaz/file17f19339b55/Azimuth_0.5.0.tar.gz' had non-zero exit status

library(Azimuth)

Error in library(Azimuth) : there is no package called 'Azimuth'

Please advise

satijalab / azimuth

Error Installing Azimuth #212

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/HDF5Array_1.30.1.tar.gz' Content type 'application/x-gzip' length 8098441 bytes (7.7 MB)

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/glmGamPoi_1.14.3.tar.gz' Content type 'application/x-gzip' length 2104554 bytes (2.0 MB)