search

egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
Other
179 stars 25 forks source link

PathfindR not supporting M3 Mac? #194

Closed jasoncrucify closed 6 months ago

jasoncrucify commented 7 months ago

Dear Developer,

we are currently working on a bioinformatic analysis using PathfindR as reference, with a Mac M3, and it is not possible to activate the packages in my Mac, could you debug and explain if it is fixed?

many thanks in advance?

egeulgen commented 7 months ago

Hello @jasoncrucify , It’s not clear what you mean by “activate”, are you having installation issues? Can you share any errors you receive, also the output of running sessionInfo() in R? For the future, I would highly recommend using the predefined issue templates as answering the relevant questions in the template helps us address the issue you’re facing faster.

jasoncrucify commented 7 months ago

Hi Thanks for your prompt reply Indeed I recently acquired a M3 Mac by cloning my previous Mac (Intel). Unfortunately it is not possible to load the package by reporting arm64 issue/errors which was never issued with my previous computer and I am wondering if this is due to the cpu issue or not.

Thanks a lot

On Thu, Mar 7, 2024 at 13:02 Ege Ulgen @.***> wrote:

Hello @jasoncrucify https://github.com/jasoncrucify , It’s not clear what you mean by “activate”, are you having installation issues? Can you share any errors you receive, also the output of running sessionInfo() in R?

— Reply to this email directly, view it on GitHub https://github.com/egeulgen/pathfindR/issues/194#issuecomment-1983366330, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKIWF7RS5ZU4A2TWXMXPFTYXBJOZAVCNFSM6AAAAABEJLD5Q2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBTGM3DMMZTGA . You are receiving this because you were mentioned.Message ID: @.***>

egeulgen commented 7 months ago

As I understand, you restored from a backup. If so, you wouldn’t be able to load the library that was previously installed for x86_64, you should install it for arm64 (which the installer will handle): install.packages("pathfindR")

if the issue persists, kindly provide more details: steps taken before the issue arose, your R configuration (output of sessionInfo())

jasoncrucify commented 7 months ago

Thanks,

Here is the error:

############################################################################## Error: package or namespace load failed for ‘pathfindR’: .onAttach failed in attachNamespace() for 'pathfindR', details: call: check_java_version() error: Java version detected but couldn't parse version from The operation couldn’t be completed. Unable to locate a Java Runtime. - Please visit http://www.java.com for information on installing Java. - In addition: Warning message: In system2(java, "-version", stderr = TRUE, stdout = TRUE) : running command ''/usr/bin/java' -version 2>&1' had status 1

I tried to uninstall the package and reinstall again following the code provided.

Many thanks for debugging.

Sincerely yours,

Le 7 mars 2024 à 14:17, Ege Ulgen @.***> a écrit :

As I understand, you restored from a backup. If so, you wouldn’t be able to load the library that was previously installed for x86_64, you should install it for arm64 (which the installer will handle): install.packages("pathfindR")

if the issue persists, kindly provide more details: steps taken before the issue arose, your R configuration (output of sessionInfo())

— Reply to this email directly, view it on GitHub https://github.com/egeulgen/pathfindR/issues/194#issuecomment-1983486698, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKIWF4WVOZCYXCLOHQH7ILYXBSH7AVCNFSM6AAAAABEJLD5Q2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBTGQ4DMNRZHA. You are receiving this because you were mentioned.

egeulgen commented 7 months ago

there seems to be an issue with Java installation/R configuration. Please follow the advice in this article and let me know if that resolves the issue. Particularly, this section to reconfigure R so that R points to the desired Java installation.

sudo R CMD javareconf
jasoncrucify commented 6 months ago

Thanks for your reply It works now your package after reinstallation of Java :) Sincerely yours

On Sat, Mar 9, 2024 at 23:39 Ege Ulgen @.***> wrote:

there seems to be an issue with Java installation/R configuration. Please follow the advice in this article https://solutions.posit.co/envs-pkgs/using-rjava/#setup-java-support-in-r and let me know if that resolves the issue. Particularly, this section to reconfigure R https://solutions.posit.co/envs-pkgs/using-rjava/#reconfigure-r so that R points to the desired Java installation.

sudo R CMD javareconf

— Reply to this email directly, view it on GitHub https://github.com/egeulgen/pathfindR/issues/194#issuecomment-1986998935, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKIWF6HINBUJAVKI36Y62TYXOFQ5AVCNFSM6AAAAABEJLD5Q2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBWHE4TQOJTGU . You are receiving this because you were mentioned.Message ID: @.***>