Closed sunabcun closed 3 years ago
sunabcun
commented
3 years ago I found that our HPC uses R3.6 version which is using old Bioconductor as well. It automatically pulls RnBeads old version which has the unfixed the ff issues. I have managed to install newer version of RnBeads and it seems to work now for this part. I will close it but keep this posting for other people who may have similar issues in the future.
Arsoy752
commented
3 years ago Hello I am facing the same problem , can you share with me how did you upgrade you rRNbeads, the version I have is RnBeads_2.6.0 Bioconductor version 3.11 (BiocManager 1.30.15), R 4.0.2 (2020-06-22)
sunabcun
commented
3 years ago Hi, I also had a hard time to figure out what is going on. So, what happen is RnBeads some old version had an issue with bigFf.Rhttps://github.com/epigen/RnBeads/blob/master/R/bigFf.R source file codes. They changed it after version 2.10 as I know. You probably used similar old version like me you can double check by searching RnBeads 2.6.0 source code and check bigFf.R file. And, if it wasn’t changed close.ff(res) to close(res) then it could be the issue. What you can do is (unfortunately) upgrading your R to >= 4.0.0 and Bioconductor as well. And then re-download RnBeads package (I checked after R4.0.0/equivalent Bioconductor version has RnBeads packages >= 2.10.0). It is quite a lot of works and I spent so long time for finding this issue. If you are using HPC like me, HPC may have really old gcc compiler so it may cause issues to download one of the important packages to install newer RnBeads. What you can do is load newer version gcc (mine was 4.8.5!!!!) or ask HPC to upgrade if you don’t have a newer gcc. It was a total nightmare… Hope It could be helpful for you.
From: @.> Sent: Wednesday, May 26, 2021 1:56 PM To: @.> Cc: Yuna @.>; State @.> Subject: Re: [epigen/RnBeads] ff function issues? (#22)
Hello I am facing the same problem , can you share with me how did you upgrade you rRNbeads, the version I have is RnBeads_2.6.0 Bioconductor version 3.11 (BiocManager 1.30.15), R 4.0.2 (2020-06-22)
— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/epigen/RnBeads/issues/22*issuecomment-848995808__;Iw!!PhOWcWs!kiERdoroa5Jt_6qggXA2FTq6iU_T9V8qNEqb4uQvfYE_lkhfQb_FmEve038RDKFFZZQ$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ALGWH6MIIPDQJNYISACH2HTTPUY4XANCNFSM45P7RHCA__;!!PhOWcWs!kiERdoroa5Jt_6qggXA2FTq6iU_T9V8qNEqb4uQvfYE_lkhfQb_FmEve038R_Pub1p8$.
Arsoy752
commented
3 years ago Hi, I also had a hard time to figure out what is going on. So, what happen is RnBeads some old version had an issue with bigFf.Rhttps://github.com/epigen/RnBeads/blob/master/R/bigFf.R source file codes. They changed it after version 2.10 as I know. You probably used similar old version like me you can double check by searching RnBeads 2.6.0 source code and check bigFf.R file. And, if it wasn’t changed close.ff(res) to close(res) then it could be the issue. What you can do is (unfortunately) upgrading your R to >= 4.0.0 and Bioconductor as well. And then re-download RnBeads package (I checked after R4.0.0/equivalent Bioconductor version has RnBeads packages >= 2.10.0). It is quite a lot of works and I spent so long time for finding this issue. If you are using HPC like me, HPC may have really old gcc compiler so it may cause issues to download one of the important packages to install newer RnBeads. What you can do is load newer version gcc (mine was 4.8.5!!!!) or ask HPC to upgrade if you don’t have a newer gcc. It was a total nightmare… Hope It could be helpful for you. From: @.> Sent: Wednesday, May 26, 2021 1:56 PM To: @.> Cc: Yuna @.>; State @.> Subject: Re: [epigen/RnBeads] ff function issues? (#22) Hello I am facing the same problem , can you share with me how did you upgrade you rRNbeads, the version I have is RnBeads_2.6.0 Bioconductor version 3.11 (BiocManager 1.30.15), R 4.0.2 (2020-06-22) — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub<https://urldefense.com/v3/https:/github.com/epigen/RnBeads/issues/22*issuecomment-848995808;Iw!!PhOWcWs!kiERdoroa5Jt_6qggXA2FTq6iU_T9V8qNEqb4uQvfYE_lkhfQb_FmEve038RDKFFZZQ$>, or unsubscribe<https://urldefense.com/v3/https:/github.com/notifications/unsubscribe-auth/ALGWH6MIIPDQJNYISACH2HTTPUY4XANCNFSM45P7RHCA;!!PhOWcWs!kiERdoroa5Jt_6qggXA2FTq6iU_T9V8qNEqb4uQvfYE_lkhfQb_FmEve038R_Pub1p8$>.
Thanks a lot for the prompt response and explanation , in my case I just downloaded an older version of "ff" package and now it is woking fine
Hi, I have tried to run my analysis in R (hpc) and I have some issues to execute my analysis. This is the code I tried to run in R and I got the ff function errors. It seems that someone had a similar issue a few months ago but I am not sure if I can fix myself since I tried to reinstall ff packages myself and it didn't work. Many thanks!
Best, Yuna