Problem to install NetCoMi

[Fla1487]

Dear all, I continued to have the following problem to install NetCoMi.

Error: Failed to install 'NetCoMi' from GitHub: ! System command 'Rcmd.exe' failed

I use windows with the last version of R package. How can fix the problem?

Thank you in advance

[stefpeschel]

Hey, Can you please provide us with the full error message? Thanks.

[Fla1487]

Here the complete message @.***

Thank you in advance

Flavio De Maio PhD Istituto di Microbiologia e Virologia Microbiota analysis & Microbial WGS Research Core Facilty, GSTeP Fondazione Policlinico Universitario A. Gemelli IRCCS L.go Agostino Gemelli, 8 00168 Roma (Italy)

Da: Stefanie @.> Inviato: giovedì 13 aprile 2023 10:31 A: @.> Cc: De Maio @.>; @.> Oggetto: Re: [stefpeschel/NetCoMi] Problem to install NetCoMi (Issue #87)

Hey, Can you please provide us with the full error message? Thanks.

— Reply to this email directly, view it on GitHubhttps://github.com/stefpeschel/NetCoMi/issues/87#issuecomment-1506565056, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANDJXTDBHUTAWGXLYRHH6ETXA62W7ANCNFSM6AAAAAAW4IDMAM. You are receiving this because you authored the thread.Message ID: @.***>

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[stefpeschel]

Dear Flavio,

I cannot see the message as I have already emailed you. Please resend the error message.

Best, Stefanie

[ep142]

Hi Stephanie, I have just installed R 4.3 and, apparently this causes problems with re-installation of NetCoMi (which worked fine with R 4.2.3). The error I am getting is: Error: Failed to install 'NetCoMi' from GitHub: Failed to install 'Biobase' from Bioc: Command failed (69) In addition: Warning messages: 1: packages ‘propr’, ‘metagMisc’ are not available for this version of R

Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 2: In system(full, intern = TRUE, ignore.stderr = quiet) : running command ''/usr/bin/git' ls-remote https://git.bioconductor.org/packages/Biobase RELEASE_3_17 2>/dev/null' had status 69

Do you think you will be able to fix this? I need to use NetCoMi in two weeks time for a course and I might need to remove R and reinstall version 4.2... :-O

[stefpeschel]

Dear Eugenio,

I have just updated my R version to 4.3 and successfully installed NetCoMi (I'm using Windows 10 with Intel i7).

Could you please try to install Biobase again using BiocManager::install("Biobase")? The missing Biobase package seems to prevent NetCoMi from being installed.

The packages propr and metagMisc do not seem to be available for R 4.3 yet, but they are not needed for NetCoMi to be installed.

A temporary workaround would also be to copy the missing packages from the old library to the new one. Then you should at least be able to install NetCoMi.

Best wishes, Stefanie

[ep142]

Dear Stephanie, sorry for forgetting to include system info. I am using a MacBook 14” with Apple M1 Pro, 16 GB RAM and MacOS 13.4 Biobase was already in my system, but, after removing it and reinstalling (which also prompted a few package updates) I successfully installed NetCoMi and loaded it. As soon as I have time I will test it. By the way, do you now if if works with the arm64 version of R? If you are interested I can test it (after I am done giving the lectures). Regards Eugenio

Prof. Eugenio Parente Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali Università degli Studi della Basilicata Viale dell’Ateneo Lucano, 10 85100 Potenza, Italy

@.*** http://web.unibas.it/parente

On 13 Jun 2023, at 00:11, Stefanie Peschel @.***> wrote:

Dear Eugenio,

I have just updated my R version to 4.3 and successfully installed NetCoMi (I'm using Windows 10 with Intel i7).

Could you please try to install Biobase again using BiocManager::install("Biobase")? The missing Biobase package seems to prevent NetCoMi from being installed.

The packages propr and metagMisc do not seem to be available for R 4.3 yet, but they are not needed for NetCoMi to be installed.

A temporary workaround would also be to copy the missing packages from the old library to the new one. Then you should at least be able to install NetCoMi.

Best wishes, Stefanie

— Reply to this email directly, view it on GitHub https://github.com/stefpeschel/NetCoMi/issues/87#issuecomment-1588177986, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGWCW3HU2OGU43FERFBBPNTXK6HZZANCNFSM6AAAAAAW4IDMAM. You are receiving this because you commented.

[stefpeschel]

Dear Eugenio,

Glad to hear that you were able to install NetCoMi. No, I haven't tested the arm64 version. I only have an older MacOS version installed on a virtual machine. So, I don't know if I could install the arm64 version. I would appreciate it if you could test it.

Best regards, Stefanie

[Fla1487]

Dear Stefanie,

I am sorry for delay. Now I have tried to re-install the package with success after the last update.

Thank you so much

Flavio De Maio PhD Istituto di Microbiologia e Virologia Microbiota analysis & Microbial WGS Research Core Facilty, GSTeP Fondazione Policlinico Universitario A. Gemelli IRCCS L.go Agostino Gemelli, 8 00168 Roma (Italy)

Da: Stefanie @.> Inviato: lunedì 17 aprile 2023 09:09 A: @.> Cc: De Maio @.>; @.> Oggetto: Re: [stefpeschel/NetCoMi] Problem to install NetCoMi (Issue #87)

Dear Flavio,

I cannot see the message as I have already emailed you. Please resend the error message.

Best, Stefanie

— Reply to this email directly, view it on GitHubhttps://github.com/stefpeschel/NetCoMi/issues/87#issuecomment-1510819097, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANDJXTASASBP2Y2MKCF6IETXBTUBXANCNFSM6AAAAAAW4IDMAM. You are receiving this because you authored the thread.Message ID: @.***>

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[KhalidIbrahim80]

Hi Stefanie, Thank you in advance I am trying to run my data through the NetCoM package but firstly i can't install NetCoM and I get below error. Just let you know that I installed R 4.3 and, apparently this causes problems with re-installation of NetCoMi.

Downloading GitHub repo stefpeschel/NetCoMi@HEAD 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Error: Failed to install 'NetCoMi' from GitHub: Git does not seem to be installed on your system. Cheers

Kalid

[stefpeschel]

Hey Kalid,

Since the error says "Git does not seem to be installed on your system", you would need to install Git on your computer. You can download Git here: https://git-scm.com/download/win.

Once Git is installed, you should be able to install NetCoMi.

Best, Stefanie

[Fla1487]

Dear Stefanie, I have shifted to MacBook Pro M2 and unfortunatly I am not able to re-install NetCoMi.

Here the error message:

****Error: Failed to install 'unknown package' from GitHub: HTTP error 403. API rate limit exceeded for 79.37.224.209. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

Rate limit remaining: 0/60 Rate limit reset at: 2023-08-03 23:01:40 UTC**

Could you help me to know what is the problem? A similar error occurs also for the dependencies

Thank you in advance To increase your GitHub API rate limit

• Use usethis::create_github_token() to create a Personal Access Token.
• Use usethis::edit_r_environ() and add the token as GITHUB_PAT.**

[ep142]

Hi all, I had promised Stephanie I would let her know if the installation worked on arm64 versions of R and bio conductor, and it does. I did not have the problems reported by Fla1487 (I have a MacBook Pro 14'' with M1 processor, year 2021). I have used these commands: library(devtools)

need to install compilers

and xcode

devtools::install_github("irinagain/mixedCCA") devtools::install_github("GraceYoon/SPRING") devtools::install_github("stefpeschel/NetCoMi", dependencies = TRUE, repos = c("https://cloud.r-project.org/", BiocManager::repositories()))

[Fla1487]

Thank you so much, I tried as you have suggested without obtaining a good result. I have also checked for git in the terminal, but it is installed. At the moment I do not have idea what it's the problem. Of course, I will report the other error messages (the final report that it is shown at the endo of each sinle failure)

[Fla1487]

Here the errors messages before that previously showed:

devtools::install_github("stefpeschel/NetCoMi",

•                      dependencies = c("Depends", "Imports", "LinkingTo"),
  

•                      repos = c("https://cloud.r-project.org/",
  

•                                BiocManager::repositories()))
  

Downloading GitHub repo stefpeschel/NetCoMi@HEAD 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ 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: Biobase (2.60.0 -> 8dc10d2d2...) [Bioc] 5: seriation (1.4.2 -> 1.5.1 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3 Downloading GitHub repo zdk123/SpiecEasi@HEAD ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/fb/c6h3lgrs2_326ch93nn3x2fm0000gn/T/Rtmpu3seS4/remotes314755784ce/zdk123-SpiecEasi-bc33288/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 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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/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: *** [SpiecEasi.so] Error 1 ERROR: compilation failed for package ‘SpiecEasi’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SpiecEasi’ Downloading GitHub repo GraceYoon/SPRING@HEAD 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: mixedCCA (1.6.2 -> 4c2b63f75...) [GitHub] 5: seriation (1.4.2 -> 1.5.1 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3 Downloading GitHub repo zdk123/SpiecEasi@HEAD Skipping SpiecEasi, it is already being installed Downloading GitHub repo zdk123/SpiecEasi@HEAD Skipping SpiecEasi, it is already being installed ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/fb/c6h3lgrs2_326ch93nn3x2fm0000gn/T/Rtmpu3seS4/remotes3143f8ae93a/GraceYoon-SPRING-3d641a4/DESCRIPTION’ ... ─ preparing ‘SPRING’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘SPRING_1.0.4.tar.gz’

ERROR: dependency ‘SpiecEasi’ is not available for package ‘SPRING’

• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SPRING’ Downloading GitHub repo zdk123/SpiecEasi@HEAD Skipping SpiecEasi, it is already being installed Downloading GitHub repo GraceYoon/SPRING@HEAD Skipping SPRING, it is already being installed ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/fb/c6h3lgrs2_326ch93nn3x2fm0000gn/T/Rtmpu3seS4/remotes31420d2cc24/stefpeschel-NetCoMi-921ee9d/DESCRIPTION’ ... ─ preparing ‘NetCoMi’: ✔ checking DESCRIPTION meta-information ... ─ installing the package to process help pages ----------------------------------- ERROR: dependencies ‘SpiecEasi’, ‘SPRING’ are not available for package ‘NetCoMi’ ─ removing ‘/private/var/folders/fb/c6h3lgrs2_326ch93nn3x2fm0000gn/T/RtmpQ5Zcat/Rinst4473561369a/NetCoMi’ ----------------------------------- ERROR: package installation failed Error: Failed to install 'NetCoMi' from GitHub: ! System command 'R' failed In addition: Warning messages: 1: In i.p(...) : installation of package ‘/var/folders/fb/c6h3lgrs2_326ch93nn3x2fm0000gn/T//Rtmpu3seS4/file3143f1e06e2/SpiecEasi_1.1.2.tar.gz’ had non-zero exit status 2: In i.p(...) : installation of package ‘/var/folders/fb/c6h3lgrs2_326ch93nn3x2fm0000gn/T//Rtmpu3seS4/file314360b79ba/SPRING_1.0.4.tar.gz’ had non-zero exit status

[Fla1487]

Finally, I followed with success this issue: https://github.com/stefpeschel/NetCoMi/issues/11 NetCoMi is installed and loaded...now I will try its activity on MacBook

Thank for the support

[stefpeschel]

Hey @Fla1487, Sorry I just read your comments. Great that it finally worked out.

So, the solutions given by @nicolereynolds1 and @CarlaCristinaUranga in issue #11 were as follows:

• Install the GNU Fortran compiler (https://mac.r-project.org/tools/) and add it to the path export PATH=$PATH:/usr/local/gfortran/bin).
• Use usethis::browse_github_pat() to create a personal access token.
• Use usethis::edit_r_environ() and add the token as GITHUB_PAT.

And after following the instructions, it worked for you?

That's good to know, because someone else had the same error saying that the rate limit had exceeded, and for him the installation worked the next day after restarting the computer. It's good to have a workaround, though.

[stefpeschel]

@ep142 Thanks a lot for testing NetCoMi on the arm64 R version. It's great to know that it works ☺️

[Fla1487]

Hi Stefanie, I did not use properly the proposed solution. I followed this solution by nicolereynolds1:

First, I had to install GNU Fortran compiler (https://mac.r-project.org/tools/) and add it to my path export PATH=$PATH:/usr/local/gfortran/bin

When I tried installing NetCoMi again, that's when I got the DESeq2 error. During the installation process I chose to update all dependent packages, so they all were updated before hitting that error. So then I installed DESeq2 separately

BiocManager::install("DESeq2")

That was successful, so then I tried NetCoMi again

devtools::install_github("stefpeschel/NetCoMi")

but skipped all the package updates, and the installation finally worked.

Da: Stefanie @.> Inviato: venerdì 4 agosto 2023 17:45 A: @.> Cc: De Maio @.>; @.> Oggetto: Re: [stefpeschel/NetCoMi] Problem to install NetCoMi (Issue #87)

Hey @Fla1487https://github.com/Fla1487, Sorry I just read your comments. Great that it finally worked out.

So, the solutions given by @nicolereynolds1https://github.com/nicolereynolds1 and @CarlaCristinaUrangahttps://github.com/CarlaCristinaUranga in issue #11https://github.com/stefpeschel/NetCoMi/issues/11 were as follows:

• Install the GNU Fortran compiler (https://mac.r-project.org/tools/) and add it to the path export PATH=$PATH:/usr/local/gfortran/bin).
• Use usethis::browse_github_pat() to create a personal access token.
• Use usethis::edit_r_environ() and add the token as GITHUB_PAT.

And after following the instructions, it worked for you?

That's good to know, because someone else had the same error saying that the rate limit had exceeded, and for him the installation worked the next day after restarting the computer. It's good to have a workaround, though.

— Reply to this email directly, view it on GitHubhttps://github.com/stefpeschel/NetCoMi/issues/87#issuecomment-1665813172, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANDJXTEUMEK7NW3OPYJVHLTXTUKILANCNFSM6AAAAAAW4IDMAM. You are receiving this because you were mentioned.Message ID: @.***>

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[ecfarrer]

Hi, I'm having a problem installing NetCoMi.

I'm using: R version 4.4.2 (2024-10-31) Platform: x86_64-apple-darwin20 Running under: macOS Sequoia 15.0

After running devtools::install_github("stefpeschel/NetCoMi", dependencies = c("Depends", "Imports", "LinkingTo"), repos = c("https://cloud.r-project.org/", BiocManager::repositories())) I am getting the error: Error: Failed to install 'NetCoMi' from GitHub: Unknown remote type: bioc Invalid bioc repo: [email protected]

There seems to be some problem with metagenomeSeq, so I tried installing it separately with BiocManager::install("metagenomeSeq",force=TRUE) but i got an error: package ‘metagenomeSeq’ is not available for Bioconductor version '3.20'

Then I tried installing metagenomeSeq with devtools::install_github("Bioc/metagenomeSeq@RELEASE_3_20") #this installs version 1.48 devtools::install_github("Bioc/metagenomeSeq@RELEASE_3_19") #this installs version 1.46

But I still get the same error message for NetCoMi installation: Error: Failed to install 'NetCoMi' from GitHub: Unknown remote type: bioc Invalid bioc repo: [email protected]

I can't seem to find metagenomeSeq version 1.47 anywhere. I'm not an expert on this, so I'm not even sure if I'm going in the right direction. Any help with be appreciated!

Thanks, Emily

[stefpeschel]

Hi Emily, I just updated NetCoMi to fix the issues with the Bioconductor packages. Could you please retry installing the package following the installation instructions in the readme?

[ecfarrer]

Hi Stefani, It worked, successfully installed. Thanks so much!