Issue when installing MetaboAnalystR on new version of R

[DirtyHarry80]

Hi there, it was impossible for me to install the package on the relatively new Macs with M1 chip. I am thankful for any clues.

I get the following error:

library(devtools) Loading required package: usethis devtools::install_github("xia-lab/MetaboAnalystR", build = TRUE, build_vignettes = FALSE) Downloading GitHub repo xia-lab/MetaboAnalystR@HEAD Skipping 9 packages not available: Biobase, pcaMethods, siggenes, MSnbase, impute, fgsea, edgeR, BiocParallel, RBGL ── R CMD build ────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/20/k4df0jqs2bggfwcr23k3mkch0000gn/T/Rtmp1Kmcr8/remotes721513967003/xia-lab-MetaboAnalystR-4620aa2/DESCRIPTION’ ... ─ preparing ‘MetaboAnalystR’: ✔ 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 ─ building ‘MetaboAnalystR_3.3.0.tar.gz’

• installing source package ‘MetaboAnalystR’ ... using staged installation libs rm -f fortran/decorana.o c/Internal_utils_batch.o c/util.o c/fastmatch.o c/nncgc.o c/mzROI.o c/xcms_binners.o /opt/R/arm64/bin/gfortran -mtune=native -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c fortran/decorana.f -o fortran/decorana.o make: /opt/R/arm64/bin/gfortran: No such file or directory make: *** [fortran/decorana.o] Error 1 ERROR: compilation failed for package ‘MetaboAnalystR’
• removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/MetaboAnalystR’ Warning message: In i.p(...) : installation of package ‘/var/folders/20/k4df0jqs2bggfwcr23k3mkch0000gn/T//Rtmp1Kmcr8/file721561460560/MetaboAnalystR_3.3.0.tar.gz’ had non-zero exit status

[lcamVz]

Have you been able to resolve this issue? @DirtyHarry80

[DirtyHarry80]

No I was unable to do it and my colleagues have also installation problems on Windows machines. Honestly, great package, but one of the most difficult to install. It seems to be a matter of luck and star alignment :)

On 28 Jul 2023, at 19:59, Lennel Camuy @.***> wrote:



Have you been able to resolve this issue? @DirtyHarry80https://github.com/DirtyHarry80

— Reply to this email directly, view it on GitHubhttps://github.com/xia-lab/MetaboAnalystR/issues/261#issuecomment-1656112746, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AM5ZOXYYHTO6RAR5VV6FJKLXSP4Y3ANCNFSM6AAAAAAVLEKR74. You are receiving this because you were mentioned.Message ID: @.***>

[gowindj]

I have encountered the same problem. Have you solved it ???

[DirtyHarry80]

Hi Everyone, no reply from @xia-lab. The issue persists. The only solution is to keep operating an old version of the code on an old version of R. If you do no have it and need to install from scratch (as my students need) you cannot make it. Sorry for not being more helpful. By the way, the issue has nothing to do with M1 chip from mac as problem persists also on windows machines.

[sheedyvet]

Following this thread as I have the same issue on a Windows machine.

[zepup]

Hey guys... I'm trying to install this on my mac Sonoma 14.0 seems like gfortran is not supporting 14... I wonder if anyone is able to install it with Sonoma 14.0???

[DirtyHarry80]

I solved my issue by completely updating the R and R studio to the newest versions; + removed completely old Python on the computer (https://www.switchingtomac.com/macos/how-to-completely-uninstall-python-on-your-mac/) and replaced it with the newest version. Believe it or not, on Mac, the problem comes from the new architecture of the processors and the fact that I transferred from old to new mac (to keep the soft etc.). Additionally, when trying to install the package, there were a lot of dependencies that were not installed automatically. I had to install them 1 by 1 from Bioconductor before re-start the installation of MetaboAnalyst.R.

[rebeelouise]

Any work arounds? I have tried everything :(