[Bioc-devel] Windows Development Build Error Message for COHCAP
cw@rden @end|ng |rom coh@org
Thu Apr 23 19:19:08 CEST 2020
Thank you very much.
Yes - I understand that there is an upcoming deadline.
If I install the version of R for Windows that you provided and I install Rtools from the following link (https://cran.r-project.org/bin/windows/Rtools/), then I can still successfully install the devel version of COHCAP.
I can also use the regular Bioconductor installer to install the devel version of COHCAP on R-devel.
My guess was that creating the temporary file in the working directory instead of another folder might help. However, since I am not getting an error message on my computer, it is a little hard to say for certain. This also sounds somewhat similar to the change that you recommended.
So, I will make the change that you described (setting the output folder the temporary directory, using tempdir()), and see if that gets rid of the error message. If not, I will continue to troubleshoot (but it sounds like that may require continuing to push updates after the deadline).
From: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Thursday, April 23, 2020 5:00 AM
To: Charles Warden <cwarden using coh.org>; 'bioc-devel using r-project.org' <bioc-devel using r-project.org>
Subject: Re: Windows Development Build Error Message for COHCAP
Thank you for your inquiry
R 4.0.0 can be downloaed from the following page. This patched page exists a few weeks out from the official R release for the patched version of R windows:
2. Landing pages can have different versions of the file for different platforms when a package will build cleanly for one platform but not another. We only propagate and make available successfully built packages.
3. You can wait a day or two if you like but realize the 3.11 release is fast approaching. If this stay ERROR and it is not fixed by monday you will have to push fixes to both a release 3.11 and the new devel branch (master branch prepping for 3.12 in fall).
4. I'll try and log on our windows builder later today to see if I can track down any additional information for you to help debug. If I find anything I will contact you about it.
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Charles Warden <cwarden using coh.org<mailto:cwarden using coh.org>>
Sent: Wednesday, April 22, 2020 12:00 PM
To: 'bioc-devel using r-project.org' <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP
I noticed that I received a few error messages in the Windows build for COHCAP:
I changed the default settings to avoid an earlier error message (again, just on Windows), but I am currently getting an error message that I am having some trouble reproducing.
Can you help me with either of the following questions?
1. I apologize for the simple question, but where can I download the Windows executable for R-4.0.0? I was able to reproduce and fix an earlier issue with R-devel (on Linux), but I was not certain how to get the error message for Windows. I have tried to reproduce the error using the devtools installation from the GitHub code (https://secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP<https://urldefense.com/v3/__https:/secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https*3A*2F*2Fgithub.com*2Fcwarden45*2FCOHCAP__;JSUlJSU!!Fou38LsQmgU!-4yYGm9SusI6BqIJRZNxpBfOemJVFMIcb81007SoLoKzPxlHIIyWD12Mh0H8$>), but that can be installed successfully (with Windows R-3.6.3).
* I am wondering if there is a chance that I might be able to wait a day or two and see if I can get a status of "OK" for all steps on all of the test servers. However, if that is true, then I am a little worried about what happens if there is a temporary error in the release version.
Thank you very much!
Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Internal Ext: 80375 | Direct: 626-218-0375
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