problems about installation

YuT95 commented 1 year ago

Hi I am not able to install NetCoMi in R studio with mac. the errors are as follows. I have tried all the answers under the issues but it didn't work. thanks!

Error: Failed to install 'NetCoMi' from GitHub: ! System command 'R' failed In addition: Warning messages: 1: In i.p(...) : installation of package ‘/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//Rtmp332LmE/filee78e3eb63f10/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status 2: In i.p(...) : installation of package ‘/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//Rtmp332LmE/filee78e41a66039/mixedCCA_1.6.2.tar.gz’ had non-zero exit status 3: In i.p(...) : installation of package ‘/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//Rtmp332LmE/filee78e3a80d0a9/SPRING_1.0.4.tar.gz’ had non-zero exit status

stefpeschel commented 1 year ago

Hi @YuT95. Apparently, the three packages SpiecEasi, SPRING, and mixedCCA cannot be installed automatically because they are only available on GitHub. Please install them manually in advance with:

devtools::install_github("zdk123/SpiecEasi")
devtools::install_github("irinagain/mixedCCA")
devtools::install_github("GraceYoon/SPRING")

The order is important because SPRING depends on mixedCCA and SpiecEasi.

YuT95 commented 1 year ago

Hi Stefanie, Thanks for your reply. but when I run it, errors are as follows:

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

library(devtools) Loading required package: usethis devtools::install_github("zdk123/SpiecEasi") Downloading GitHub repo @.*** ✔ checking for file ‘/private/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T/RtmpdVzYNU/remotesd01e75318fc0/zdk123-SpiecEasi-41448ad/DESCRIPTION’ ... ─ preparing ‘SpiecEasi’: ✔ 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 Removed empty directory ‘SpiecEasi/inst’ ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘SpiecEasi_1.1.2.tar.gz’

installing source package ‘SpiecEasi’ ... 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ADMM.cpp -o ADMM.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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matops.cpp -o matops.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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sqrtNewton.cpp -o sqrtNewton.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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c svthresh.cpp -o svthresh.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 SpiecEasi.so ADMM.o RcppExports.o matops.o sqrtNewton.o svthresh.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: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lemutls_w clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [SpiecEasi.so] Error 1 ERROR: compilation failed for package ‘SpiecEasi’
removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/SpiecEasi’ Warning message: In i.p(...) : installation of package ‘/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//RtmpdVzYNU/filed01e3e6530ad/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

devtools::install_github("irinagain/mixedCCA") Downloading GitHub repo @.*** ✔ checking for file ‘/private/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T/RtmpdVzYNU/remotesd01e6e1bab77/irinagain-mixedCCA-4c2b63f/DESCRIPTION’ ... ─ preparing ‘mixedCCA’: ✔ 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 ‘mixedCCA_1.6.2.tar.gz’
installing source package ‘mixedCCA’ ... 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_w1w2.cpp -o find_w1w2.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 mixedCCA.so RcppExports.o find_w1w2.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: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lemutls_w clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [mixedCCA.so] Error 1 ERROR: compilation failed for package ‘mixedCCA’
removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/mixedCCA’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/mixedCCA’ Warning message: In i.p(...) : installation of package ‘/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//RtmpdVzYNU/filed01e5a964a1a/mixedCCA_1.6.2.tar.gz’ had non-zero exit status Best, Yu

At 2022-11-22 16:11:41, "Stefanie Peschel" @.***> wrote:

Hi @YuT95. Apparently, the three packages SpiecEasi, SPRING, and mixedCCA cannot be installed automatically because they are only available on GitHub. Please install them manually in advance with:

devtools::install_github("zdk123/SpiecEasi") devtools::install_github("irinagain/mixedCCA") devtools::install_github("GraceYoon/SPRING")

The order is important because SPRING depends on mixedCCA and SpiecEasi.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

stefpeschel commented 1 year ago

Sorry, I forgot that mixedCCA is available on CRAN as well. So please install the package from CRAN as first step: install.packages("mixedCCA")

Then, install SpiecEasi: devtools::install_github("zdk123/SpiecEasi") and SPRING as last step: devtools::install_github("GraceYoon/SPRING")

I assume it's a general problem with installing packages from GitHub on Mac. Please ensure that you're using the latest devtools version.

YuT95 commented 1 year ago

Hi, sorry it still didn't work...

install.packages("devtools") Error in install.packages : Updating loaded packages

Restarting R session...

install.packages("devtools") trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz' Content type 'application/octet-stream' length 421790 bytes (411 KB)

downloaded 411 KB

The downloaded binary packages are in /var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//RtmprtWFa8/downloaded_packages

update.packages("devtools") install.packages("mixedCCA") trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/mixedCCA_1.6.2.tgz' Content type 'application/octet-stream' length 538272 bytes (525 KB)

downloaded 525 KB

The downloaded binary packages are in /var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//RtmprtWFa8/downloaded_packages

library("devtools") Loading required package: usethis devtools::install_github("zdk123/SpiecEasi") Downloading GitHub repo @.*** ✔ checking for file ‘/private/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T/RtmprtWFa8/remotes176ec3a3ab971/zdk123-SpiecEasi-41448ad/DESCRIPTION’ ... ─ preparing ‘SpiecEasi’: ✔ 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 Removed empty directory ‘SpiecEasi/inst’ ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘SpiecEasi_1.1.2.tar.gz’

installing source package ‘SpiecEasi’ ... 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ADMM.cpp -o ADMM.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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matops.cpp -o matops.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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sqrtNewton.cpp -o sqrtNewton.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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c svthresh.cpp -o svthresh.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 SpiecEasi.so ADMM.o RcppExports.o matops.o sqrtNewton.o svthresh.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: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lemutls_w clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [SpiecEasi.so] Error 1 ERROR: compilation failed for package ‘SpiecEasi’
removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/SpiecEasi’ Warning message: In i.p(...) : installation of package ‘/var/folders/wx/xprxkc2j53j4qqfk46d5cy300000gn/T//RtmprtWFa8/file176ec6c25b674/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

At 2022-11-22 17:52:21, "Stefanie Peschel" @.***> wrote:

Sorry, I forgot that mixedCCA is available on CRAN as well. So please install the package from CRAN as first step: install.packages("mixedCCA")

Then, install SpiecEasi: devtools::install_github("zdk123/SpiecEasi") and SPRING as last step: devtools::install_github("GraceYoon/SPRING")

I assume it's a general problem with installing packages from GitHub on Mac. Please ensure that you're using the latest devtools version.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

stefpeschel commented 1 year ago

There is already an open issue for SpiecEasi: https://github.com/zdk123/SpiecEasi/issues/225. This seems to be the same error you get. You could maybe comment that you have the same issue.

I'm really sorry but this issue is not directly NetCoMi related and I don't know how to solve it either.

daydream-boost commented 1 year ago

Hi, @YuT95 You can use conda/mamba to install NetCoMi easily on MacOS.

stefpeschel / NetCoMi

problems about installation #75

install.packages("devtools") trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz' Content type 'application/octet-stream' length 421790 bytes (411 KB)

update.packages("devtools") install.packages("mixedCCA") trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/macosx/big-sur-arm64/contrib/4.2/mixedCCA_1.6.2.tgz' Content type 'application/octet-stream' length 538272 bytes (525 KB)