Unable to Install SpiecEasi

[kbazany]

Hello,

I am having trouble installing SpiecEasi. I have MASS, pulsar, and huge. Are there other dependencies I'm missing? I am working on a MacOS 12.6. The errors I am getting are "directory not found" and "compilation failed"

Here is the full error message:

install_github("zdk123/SpiecEasi") Downloading GitHub repo zdk123/SpiecEasi@HEAD ✔ checking for file ‘/private/var/folders/fw/zd4dlkh57zsc9c9tzdzz_8cw0000gn/T/RtmpfIXk3W/remotes5f647ac0aabe/zdk123-SpiecEasi-c463727/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ADMM.cpp -o ADMM.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c matops.cpp -o matops.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sqrtNewton.cpp -o sqrtNewton.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c svthresh.cpp -o svthresh.o clang++ -mmacosx-version-min=10.13 -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/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0' ld: warning: directory not found for option '-L/usr/local/gfortran/lib' ld: library not found for -lgfortran 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/Resources/library/SpiecEasi’ Warning message: In i.p(...) : installation of package ‘/var/folders/fw/zd4dlkh57zsc9c9tzdzz_8cw0000gn/T//RtmpfIXk3W/file5f647f09dee7/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

Thank you!

[YuT95]

Hi kbazany, I have similar errors with, could i ask if you have solved this problems?

thank you!

[kbazany]

No sorry! I haven't gotten an answer yet! I'll let you know if I figure it out!

---

From: YuT95 @.> Sent: Tuesday, November 22, 2022 7:31 AM To: zdk123/SpiecEasi @.> Cc: Bazany,Kate @.>; Author @.> Subject: Re: [zdk123/SpiecEasi] Unable to Install SpiecEasi (Issue #225)

Caution: EXTERNAL Sender

Hi kbazany, I have similar errors with, could i ask if you have solved this problems?

thank you!

— Reply to this email directly, view it on GitHubhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fzdk123%2FSpiecEasi%2Fissues%2F225%23issuecomment-1323767364&data=05%7C01%7CKate.Bazany%40colostate.edu%7C36466361624d4207766108dacc963e7b%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C638047242926182101%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yJwYSd0r7NZCnZto5E5kCWxcMVHr7pRBWWkqDd5rTkg%3D&reserved=0, or unsubscribehttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAVQ5H6RTDUAJTZGUZ3ZYT5LWJTKMBANCNFSM6AAAAAASDZXU7Q&data=05%7C01%7CKate.Bazany%40colostate.edu%7C36466361624d4207766108dacc963e7b%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C638047242926182101%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=l3Q7CLN%2BVvfCSBOA2VSxQ4ghx3xL7OwAM5sIt4fNUec%3D&reserved=0. You are receiving this because you authored the thread.Message ID: @.***>

[zdk123]

@kbazany it looks like fortran is missing. Are you on MacOS? See https://www.r-bloggers.com/2021/03/gfortran-support-for-r-on-macos-2/

[LauraBMar]

Hi,

I am also having the same problem.

I want to install NetCoMi in my MacOS, and I followed the advice to install first mixed CCA, and then SpiecEasi.

When I try to install SpiecEasi, it firsts ask me to update these packages; 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: igraph (1.5.0.1 -> 1.5.1 ) [CRAN] 5: RcppArmad... (0.12.4.1.0 -> 0.12.6.1.0) [CRAN]

And then results in this error;

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: *** [SpiecEasi.so] Error 1 ERROR: compilation failed for package ‘SpiecEasi’

• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SpiecEasi’ Warning message: In i.p(...) : installation of package ‘/var/folders/v2/jm6fgmfn6v9dtmd95l92nl600000gn/T//RtmpDMxP6Y/file56a34c2cf80b/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status

I don´t know what should I do. Is there a known solution by now?

Thanks in advance for your help,

Laura

[ep142]

Has anyone tried to install on Mac running the arm64 version of R? I am using SpiecEasi without any problem but I had to stick with the Intel version of R, which is a pity, since BioConductor now supports (generally speaking) arm64 processors