[Bioc-devel] Windows Development Build Error Message for COHCAP

Thu Apr 23 19:19:08 CEST 2020

Hi Lori,

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).

Thanks again!

Sincerely,
Charles

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:

https://cran.r-project.org/bin/windows/base/rpatched.html<https://urldefense.com/v3/__https:/cran.r-project.org/bin/windows/base/rpatched.html__;!!Fou38LsQmgU!-4yYGm9SusI6BqIJRZNxpBfOemJVFMIcb81007SoLoKzPxlHIIyWD5uBoQIj$>

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.

Cheers,

Lori Shepherd

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

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FCOHCAP%2Ftokay2-buildsrc.html<https://urldefense.com/v3/__http:/secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http*3A*2F*2Fbioconductor.org*2FcheckResults*2Fdevel*2Fbioc-LATEST*2FCOHCAP*2Ftokay2-buildsrc.html__;JSUlJSUlJSU!!Fou38LsQmgU!-4yYGm9SusI6BqIJRZNxpBfOemJVFMIcb81007SoLoKzPxlHIIyWD6vpzrwV$>

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$>), but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different (http://secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FCOHCAP.html<https://urldefense.com/v3/__http:/secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http*3A*2F*2Fbioconductor.org*2Fpackages*2F3.11*2Fbioc*2Fhtml*2FCOHCAP.html__;JSUlJSUlJSU!!Fou38LsQmgU!-4yYGm9SusI6BqIJRZNxpBfOemJVFMIcb81007SoLoKzPxlHIIyWDwIYeCLq$>), where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error message in 1.33.1, and I made an intermediate change before changing the defaults to avoid the error message.  However, the strange thing was that I thought I saw an "OK" status while I was waiting for the 1.33.3 version to appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of the packages get re-built, regardless of whether an update is uploaded?
     *   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!

Sincerely,
Charles
Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375

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