Re: [Bioc-devel] MAEndToEnd workflow dropped from the build system?
*ahem*, yes I actually did not run R CMD check before pushing, sorry! thanks a lot for your prompt response Lori! Best wishes, Bernd On Do, 2018-08-23 at 11:08 +, Shepherd, Lori wrote: > I think this may be do to a malformed DESCRIPTION file that was > committed in either 1.99.2 or 1.99.3. When I tried to build the > package I got > > Workflows$ R CMD build maEndToEnd/ > * checking for file 'maEndToEnd/DESCRIPTION' ...Error : file > '/home/lori/b/Workflows/maEndToEnd/DESCRIPTION' is not in valid DCF > format > EXISTS but not correct format > > I think this is because there were newline breaks in the description > field of the DESCRIPTION file. > > I pushed an updated and hopefully it will propagate on tomorrow's > build of the workflows. I will try and keep an eye on this to make > sure it corrected the issue but if you still do not see the package > propagating next week please reach back out. > > > Lori Shepherd > Bioconductor Core Team > Roswell Park Cancer Institute > Department of Biostatistics & Bioinformatics > Elm & Carlton Streets > Buffalo, New York 14263 > From: Bioc-devel on behalf of > Bernd Klaus > Sent: Thursday, August 23, 2018 4:15:17 AM > To: bioc-devel > Subject: [Bioc-devel] MAEndToEnd workflow dropped from the build > system? > > Dear Bioc-Team, > > it seem like our MyEndToEnd workflow has somehow > been dropped from the build system, the last build is > from Aug 8th: > > http://bioconductor.org/checkResults/3.8/workflows-LATEST/maEndToEnd/ > > at version 1.99.1 > > However, the current version is 1.99.4, the last commit is > 135704a by Lori. See here on github: > > https://github.com/b-klaus/maEndToEnd/commit/135704a1ad01025bef967666 > 31 > f5bbf87d874f99 > > For some reason this is not propagated to the build system ... > > Thanks a lot for your help! > > Bernd > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the > employee or agent responsible for the delivery of this message to the > intended recipient(s), you are hereby notified that any disclosure, > copying, distribution, or use of this email message is prohibited. If > you have received this message in error, please notify the sender > immediately by e-mail and delete this email message from your > computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Major update to rhdf5 and Rhdf5lib
Thanks for your work on this, Mike! On Thu., 23 Aug. 2018, 9:46 pm Mike Smith, wrote: > Hi all, > > I've just submitted updated versions of rhdf5 (2.25.7) and Rhdf5lib (1.3.2) > to the BioC devel branch. These represent a significant change as the > underlying version of HDF5 has now changed from 1.8.19 to 1.10.2. This has > been done in response to an increasing prevalence of files that cannot be > read with HDF5 1.8. > > The most significant change from an R package point of view is that the > internal handles for HDF5 objects switched to being 64bit integers, which > are more tricky to deal with directly in R. Hopefully I have caught and > handled these cases, and the packages are building/passing check for me on > Linux and Windows. I have also run the tests distributed with HDF5Array, > DelayedArray, and DelayedMatrixStats and all seem fine. However, if you > encounter a new and exciting error please reply here or open an issue at > https://github.com/grimbough/rhdf5/issues > > HDF5 1.10 provides a number of new features that you can read about at > https://support.hdfgroup.org/HDF5/docNewFeatures/ If you need access to > one > of these and it's not obviously available via rhdf5 then again please > contact me & I'll prioritise things accordingly. > > Thanks, > > Mike > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Major update to rhdf5 and Rhdf5lib
Hi all, I've just submitted updated versions of rhdf5 (2.25.7) and Rhdf5lib (1.3.2) to the BioC devel branch. These represent a significant change as the underlying version of HDF5 has now changed from 1.8.19 to 1.10.2. This has been done in response to an increasing prevalence of files that cannot be read with HDF5 1.8. The most significant change from an R package point of view is that the internal handles for HDF5 objects switched to being 64bit integers, which are more tricky to deal with directly in R. Hopefully I have caught and handled these cases, and the packages are building/passing check for me on Linux and Windows. I have also run the tests distributed with HDF5Array, DelayedArray, and DelayedMatrixStats and all seem fine. However, if you encounter a new and exciting error please reply here or open an issue at https://github.com/grimbough/rhdf5/issues HDF5 1.10 provides a number of new features that you can read about at https://support.hdfgroup.org/HDF5/docNewFeatures/ If you need access to one of these and it's not obviously available via rhdf5 then again please contact me & I'll prioritise things accordingly. Thanks, Mike [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] MAEndToEnd workflow dropped from the build system?
I think this may be do to a malformed DESCRIPTION file that was committed in either 1.99.2 or 1.99.3. When I tried to build the package I got Workflows$ R CMD build maEndToEnd/ * checking for file 'maEndToEnd/DESCRIPTION' ...Error : file '/home/lori/b/Workflows/maEndToEnd/DESCRIPTION' is not in valid DCF format EXISTS but not correct format I think this is because there were newline breaks in the description field of the DESCRIPTION file. I pushed an updated and hopefully it will propagate on tomorrow's build of the workflows. I will try and keep an eye on this to make sure it corrected the issue but if you still do not see the package propagating next week please reach back out. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Bernd Klaus Sent: Thursday, August 23, 2018 4:15:17 AM To: bioc-devel Subject: [Bioc-devel] MAEndToEnd workflow dropped from the build system? Dear Bioc-Team, it seem like our MyEndToEnd workflow has somehow been dropped from the build system, the last build is from Aug 8th: http://bioconductor.org/checkResults/3.8/workflows-LATEST/maEndToEnd/ at version 1.99.1 However, the current version is 1.99.4, the last commit is 135704a by Lori. See here on github: https://github.com/b-klaus/maEndToEnd/commit/135704a1ad01025bef96766631 f5bbf87d874f99 For some reason this is not propagated to the build system ... Thanks a lot for your help! Bernd ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] MAEndToEnd workflow dropped from the build system?
Dear Bioc-Team, it seem like our MyEndToEnd workflow has somehow been dropped from the build system, the last build is from Aug 8th: http://bioconductor.org/checkResults/3.8/workflows-LATEST/maEndToEnd/ at version 1.99.1 However, the current version is 1.99.4, the last commit is 135704a by Lori. See here on github: https://github.com/b-klaus/maEndToEnd/commit/135704a1ad01025bef96766631 f5bbf87d874f99 For some reason this is not propagated to the build system ... Thanks a lot for your help! Bernd ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
