Dear Hervé, You are right. I found the issue in rtracklayer and made a pull request with a fix. https://github.com/lawremi/rtracklayer/pull/1
Thanks for your help. Best, Markus On Tue, 12 Sep 2017 at 18:01 Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Markus, > > The class cache issue is just a warning here and is distracting. > > What seems to break deepblue_liftover() is a recent > change to rtracklayer::import.chain. Looks like commit > a3c4308d928290700c6326eabda8dea4a96146e3 from Sep 4 might > be the culprit. > > Cheers, > H. > > On 09/12/2017 06:29 AM, Markus List wrote: > > Dear all, > > > > Our DeepBlueR package is currently not passing R CMD check in devel > because > > of a class cache issue: > > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_DeepBlueR_tokay1-2Dchecksrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=16yr6qe7_7dlWZwyc2Gc-3FYwTUMp05_zrQefmUS5-s&e= > > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_44295792_setoldclassxts-2Dcausing-2Dproblems-2Din-2Da-2Dcustom-2Dr-2Dpackage&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=zpx_S8s7mXlN0c6p-TWbtP_dye8qcH566wopHfbZq6c&e= > > > > > > 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> <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> <0681%2093253008> > >>>> Email: felipe.albre...@mpi-inf.mpg.de > >>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__felipealbrecht.github.io&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=5PsLbRsqSNF8p-aFTTuQCcBfgwWqTvD3zevglr2b5EE&e= > >>>> > >>>> -------- 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): > >>>> > >>>> > >>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.6_bioc-2DLATEST_DeepBlueR_malbec1-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=HBR9LT3bziKoBkC1YrtJbJJhDmCm56qZ-0P_7faa7A4&e= > >>>> > >>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=-PxcuWWc9WNLZR5Q0iP67tH5aI29Y2ko8u_PDcIIONk&e= > >>>> > >>>> > >>>> > >>>> 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. Thank you. > >> > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sqCu4UFxGa-qRfOicVS9ybuVLjBf9iBoz9K51rrpri8&s=Iwss_CBq6lciZgUI67nVIHI57fya-eONuTlZ2VrxcNA&e= > > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
