Hi, This Friday, October 6, is the last day to submit new packages for inclusion in BioC 3.6. Packages submitted by Friday still need to complete the review process before the release but we'll do our best to get them in. Packages submitted after the deadline will be included in the new devel, BioC 3.7. http://www.bioconductor.org/developers/release-schedule/ Valerie 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] Bioconductor 3.6 release: deadline for new packages
5 messages · Obenchain, Valerie, Ludwig Geistlinger, Lucas Schiffer +1 more
Hi, R CMD check of the devel version of my package lately started to trigger a warning: http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html * checking whether package ?EnrichmentBrowser? can be installed ... WARNING Found the following significant warnings: Warning: no function found corresponding to methods exports from ?Organism.dplyr? for: ?supportedFilters? See ?/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out? for details. I am not quite sure how to deal with that. Any advice? Thanks, Ludwig
Dr. Ludwig Geistlinger eMail: Ludwig.Geistlinger at bio.ifi.lmu.de > Hi, > > This Friday, October 6, is the last day to submit new packages for > inclusion in BioC 3.6. Packages submitted by Friday still need to complete > the review process before the release but we'll do our best to get them > in. Packages submitted after the deadline will be included in the new > devel, BioC 3.7. > > http://www.bioconductor.org/developers/release-schedule/ > > Valerie > > > 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 at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel >
Hello, I think this is related to GSEABase, I noticed this warning when updating packages today. * installing *source* package 'GSEABase' ... ** R ** inst ** preparing package for lazy loading Warning: no function found corresponding to methods exports from 'Organism.dplyr' for: 'supportedFilters' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: no function found corresponding to methods exports from 'Organism.dplyr' for: 'supportedFilters' * DONE (GSEABase) Perhaps GSEABase or Organism.dplyr needs a patch. Thanks, Lucas
On Oct 3, 2017, at 10:54, Ludwig Geistlinger <Ludwig.Geistlinger at bio.ifi.lmu.de> wrote: Hi, R CMD check of the devel version of my package lately started to trigger a warning: http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html * checking whether package ?EnrichmentBrowser? can be installed ... WARNING Found the following significant warnings: Warning: no function found corresponding to methods exports from ?Organism.dplyr? for: ?supportedFilters? See ?/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out? for details. I am not quite sure how to deal with that. Any advice? Thanks, Ludwig -- Dr. Ludwig Geistlinger eMail: Ludwig.Geistlinger at bio.ifi.lmu.de
Hi, This Friday, October 6, is the last day to submit new packages for inclusion in BioC 3.6. Packages submitted by Friday still need to complete the review process before the release but we'll do our best to get them in. Packages submitted after the deadline will be included in the new devel, BioC 3.7. http://www.bioconductor.org/developers/release-schedule/ Valerie 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
A recent change that was made to GSEABase seems to be the source of the problem. We're looking at it now.
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Lucas Schiffer <schiffer.lucas at gmail.com>
Sent: Tuesday, October 3, 2017 2:29:51 PM
To: Ludwig Geistlinger
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Organism.dplyr::supportedFilters warning
Sent: Tuesday, October 3, 2017 2:29:51 PM
To: Ludwig Geistlinger
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Organism.dplyr::supportedFilters warning
Hello, I think this is related to GSEABase, I noticed this warning when updating packages today. * installing *source* package 'GSEABase' ... ** R ** inst ** preparing package for lazy loading Warning: no function found corresponding to methods exports from 'Organism.dplyr' for: 'supportedFilters' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: no function found corresponding to methods exports from 'Organism.dplyr' for: 'supportedFilters' * DONE (GSEABase) Perhaps GSEABase or Organism.dplyr needs a patch. Thanks, Lucas > On Oct 3, 2017, at 10:54, Ludwig Geistlinger <Ludwig.Geistlinger at bio.ifi.lmu.de> wrote: > > Hi, > > R CMD check of the devel version of my package lately started to trigger a > warning: > > http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html > > > * checking whether package ?EnrichmentBrowser? can be installed ... WARNING > Found the following significant warnings: > > Warning: no function found corresponding to methods exports from > ?Organism.dplyr? for: ?supportedFilters? > > See > ?/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out? > for details. > > I am not quite sure how to deal with that. > Any advice? > > Thanks, > Ludwig > > -- > Dr. Ludwig Geistlinger > eMail: Ludwig.Geistlinger at bio.ifi.lmu.de > >> Hi, >> >> This Friday, October 6, is the last day to submit new packages for >> inclusion in BioC 3.6. Packages submitted by Friday still need to complete >> the review process before the release but we'll do our best to get them >> in. Packages submitted after the deadline will be included in the new >> devel, BioC 3.7. >> >> http://www.bioconductor.org/developers/release-schedule/ >> >> Valerie >> >> >> 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 at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at 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.
1 day later
We've updated GSEABase on devel yesterday so that it should build correctly. This will fix the warning that was being sent off by EnrichmentBrowser. The changes may take a few days to propagate.
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Van Twisk, Daniel <Daniel.VanTwisk at RoswellPark.org>
Sent: Tuesday, October 3, 2017 3:08:36 PM
To: Lucas Schiffer; Ludwig Geistlinger
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Organism.dplyr::supportedFilters warning
Sent: Tuesday, October 3, 2017 3:08:36 PM
To: Lucas Schiffer; Ludwig Geistlinger
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Organism.dplyr::supportedFilters warning
A recent change that was made to GSEABase seems to be the source of the problem. We're looking at it now. ________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Lucas Schiffer <schiffer.lucas at gmail.com> Sent: Tuesday, October 3, 2017 2:29:51 PM To: Ludwig Geistlinger Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Organism.dplyr::supportedFilters warning Hello, I think this is related to GSEABase, I noticed this warning when updating packages today. * installing *source* package 'GSEABase' ... ** R ** inst ** preparing package for lazy loading Warning: no function found corresponding to methods exports from 'Organism.dplyr' for: 'supportedFilters' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: no function found corresponding to methods exports from 'Organism.dplyr' for: 'supportedFilters' * DONE (GSEABase) Perhaps GSEABase or Organism.dplyr needs a patch. Thanks, Lucas > On Oct 3, 2017, at 10:54, Ludwig Geistlinger <Ludwig.Geistlinger at bio.ifi.lmu.de> wrote: > > Hi, > > R CMD check of the devel version of my package lately started to trigger a > warning: > > http://bioconductor.org/checkResults/devel/bioc-LATEST/EnrichmentBrowser/malbec1-checksrc.html > > > * checking whether package ?EnrichmentBrowser? can be installed ... WARNING > Found the following significant warnings: > > Warning: no function found corresponding to methods exports from > ?Organism.dplyr? for: ?supportedFilters? > > See > ?/home/biocbuild/bbs-3.6-bioc/meat/EnrichmentBrowser.Rcheck/00install.out? > for details. > > I am not quite sure how to deal with that. > Any advice? > > Thanks, > Ludwig > > -- > Dr. Ludwig Geistlinger > eMail: Ludwig.Geistlinger at bio.ifi.lmu.de > >> Hi, >> >> This Friday, October 6, is the last day to submit new packages for >> inclusion in BioC 3.6. Packages submitted by Friday still need to complete >> the review process before the release but we'll do our best to get them >> in. Packages submitted after the deadline will be included in the new >> devel, BioC 3.7. >> >> http://www.bioconductor.org/developers/release-schedule/ >> >> Valerie >> >> >> 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 at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at 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]] 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.