Dear all, Our DeepBlueR package is currently not passing R CMD check in devel because of a class cache issue:
http://bioconductor.org/checkResults/devel/bioc-LATEST/DeepBlueR/tokay1-checksrc.html Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Also defined by ‘filehash’ Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘path’ for signature ‘"file"’ Calls: deepblue_liftover ... import -> .local -> path.expand -> path -> <Anonymous> Execution halted I suspect this is caused by a conflict between filehashdb and BiocGenerics which both use setOldClass with "file" to S4ify it. setOldClass has caused trouble for other people, too: https://stackoverflow.com/questions/44295792/setoldclassxts-causing-problems-in-a-custom-r-package Still, don't know is why this suddenly leads to an error in devel and how to fix it. Any ideas? Best, Markus On Mon, 11 Sep 2017 at 11:21 Markus List <markus.l...@mpi-inf.mpg.de> wrote: > Hi Nitesh, > > Thanks for looking into it. Unfortunately, I still can't access the > repository since I was using a DSA key which was previously mentioned here > as not supported. I thus generated an RSA key and added it to github. Will > newly added github keys be automatically imported? If not could you please > add my new key (github username mlist). > > Best, > Markus > > > On Fri, 8 Sep 2017 at 15:12 Turaga, Nitesh <nitesh.tur...@roswellpark.org> > wrote: > >> Hi Markus, >> >> Your SSH key has been accepted, but you don’t have access to the >> repository because the SVN system did not know you have access rights to >> this package. >> >> I’ll give you access rights to that package. >> >> Best >> >> Nitesh >> >> > On Sep 8, 2017, at 7:34 AM, Shepherd, Lori >> <lori.sheph...@roswellpark.org> wrote: >> > >> > >> > >> > Lori Shepherd >> > Bioconductor Core Team >> > Roswell Park Cancer Institute >> > Department of Biostatistics & Bioinformatics >> > Elm & Carlton Streets >> > Buffalo, New York 14263 >> > >> > >> > From: Markus List <markus.l...@mpi-inf.mpg.de> >> > Sent: Friday, September 8, 2017 4:31 AM >> > To: Shepherd, Lori; Felipe Albrecht >> > Subject: Re: failing Bioconductor package DeepBlueR >> > >> > Dear Lori, >> > >> > Since Felipe is on vacation I wanted to look into this issue but I can >> not push any changes to the new git repository. I tried to get my SSH keys >> accepted twice (August 18 and 22) for this by submitting my github id in >> the google form you provide but I have not received any response in . Can >> you help me out? My github id is 'mlist'. >> > >> > Best, >> > Markus >> > >> > >> > -- >> > Markus List >> > Postdoc, Computational Biology & Applied Algorithmics >> > Associate Editor, BMC Systems Biology >> > Max-Planck Institute for Informatics >> > Saarland Informatics Campus >> > Building E1.4, Room 516, 66123 Saarbrücken, Germany >> > E-mail: markus.l...@mpi-inf.mpg.de >> > Phone: +49 681 93253016 <0681%2093253016> >> > Twitter: @itisalist >> > >> > On Thu, 7 Sep 2017 at 13:15 Shepherd, Lori < >> lori.sheph...@roswellpark.org> wrote: >> > Ok. Thank you very much for looking into this. >> > >> > Lori Shepherd >> > Bioconductor Core Team >> > Roswell Park Cancer Institute >> > Department of Biostatistics & Bioinformatics >> > Elm & Carlton Streets >> > Buffalo, New York 14263 >> > From: Felipe Albrecht <felipe.albre...@mpi-inf.mpg.de> >> > Sent: Thursday, September 7, 2017 2:30:10 AM >> > To: Shepherd, Lori; markus.l...@mpi-inf.mpg.de >> > >> > Subject: Re: failing Bioconductor package DeepBlueR >> > Hello Lori, >> > Since the problem is only in the devel branch, I will fix this issue >> during next week because I'm out of office right now. >> > >> > Thank you for informing! >> > Felipe Albrecht >> > >> > >> > >> > -- >> > Max Planck Institute for Informatics >> > Computational Biology and Applied Algorithmics Department >> > Campus E 1.4 >> > Room 508 >> > 66123 Saarbrücken >> > Germany >> > Phone: +49 (681) 9325 3008 <0681%2093253008> >> > Email: felipe.albre...@mpi-inf.mpg.de >> > http://felipealbrecht.github.io >> > >> > -------- Original message -------- >> > From: "Shepherd, Lori" <lori.sheph...@roswellpark.org> >> > Date: 06/09/2017 20:56 (GMT+09:00) >> > To: felipe.albre...@mpi-inf.mpg.de, markus.l...@mpi-inf.mpg.de >> > Subject: failing Bioconductor package DeepBlueR >> > >> > Dear DeepBlueR maintainer, >> > >> > I'd like to bring to your attention that the DeepBlueR package is >> failing to pass 'R CMD build' on all platforms in the devel version of >> Bioconductor (i.e. BioC 3.6): >> > >> > >> http://bioconductor.org/checkResults/3.6/bioc-LATEST/DeepBlueR/malbec1-buildsrc.html >> > >> > Would you mind taking a look at this? Don't hesitate to ask on the >> bioc-devel mailing list if you have any question or need help. >> > >> > If no action is taken over the next few weeks we will begin the >> deprecation process for your package. Thank you for your time and effort. >> > >> > >> > Thanks for your contribution to Bioconductor. >> > >> > Pleae be advised that Bioconductor has switched from svn to Git. Some >> helpful >> > links can be found here: >> > https://bioconductor.org/developers/how-to/git/ >> > >> > >> > >> > Lori Shepherd >> > Bioconductor Core Team >> > Roswell Park Cancer Institute >> > Department of Biostatistics & Bioinformatics >> > Elm & Carlton Streets >> > Buffalo, New York 14263 >> > 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. >> >> >> >> 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. 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