conda activate error message

[ryao-mdanderson]

Dear CountCorrect author:

When do conda activate, I find the following error message, actually it happens during the installation, is this critical? Thanks!

(base) [user ~]$ conda activate countcorrect
ERROR: CONDA_BUILD_SYSROOT or SDKROOT has to be set for cross-compiling
bash: xcrun: command not found...
-bash: /meson_cross_file.txt: Permission denied
-bash: /meson_cross_file.txt: Permission denied
-bash: /meson_cross_file.txt: Permission denied
-bash: /meson_cross_file.txt: Permission denied
-bash: /meson_cross_file.txt: Permission denied

[ryao-mdanderson]

@VasylVaskivskyi @AlexanderAivazidis : May you please advise? thank you.

[AlexanderAivazidis]

Hi!
Is this the first time you work with conda environments? Do you have other conda environments that you can use successfully? I basically wonder if this is an error specific to CountCorrect, or maybe more related to conda and your computing environment in general. Also can you successfully use CountCorrect despite of this error? If yes, then I think you don't have to worry about it.

[VasylVaskivskyi]

Hi @ryao-mdanderson , quick search for your error bash: xcrun: command not found... showed that you may need to run this command xcode-select --install , or follow instructions in this answer https://apple.stackexchange.com/a/321875 .
Alternatively, you could have a problem with permission to access the directory in which you installed Conda. So you can try to reinstall it (create a new environment) on different machine and check again if the package works.

[ryao-mdanderson]

Dear author, Thank you for your reply. This is the error specific to CountCorrect, I have been working with multiple conda environments in the past. Rong

[AlexanderAivazidis]

Actually I just checked and I get the same error! It never seems to have been a problem, so you don't need to worry about it.

[AlexanderAivazidis]

But I will still investigate more what this is about.

[ryao-mdanderson]

@AlexanderAivazidis Thank you!
I was installing this on our institution HPC cluster, OS RHEL 7.9 . I experiment this in my home directory first, and seeing this. Thank you for investigating this.

[ryao-mdanderson]

@VasylVaskivskyi Thank you for your reply. I am sure I have the permission to access conda contents that I installed. I did not use xcode, this command xcode-select --install is confusing to me, I will wait and see.