Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9
Hi Herve, Thanks! just updated the file. Thanks, Qiang From: Pages, Herve Sent: Monday, October 21, 2019 1:07 PM To: Hu, Qiang ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9 Hi Qiang, Any reason why you use: UnsupportedPlatforms: win64, win32 and not just: UnsupportedPlatforms: win in your .BBSoptions file? Also make sure to have a line terminator: hpages@spectre:~/RcwlPipelines$ file .BBSoptions .BBSoptions: ASCII text, with no line terminators The lack of line terminator might be breaking the code that parses the file. Thanks, H. On 10/21/19 09:23, Hu, Qiang wrote: > Hi, > > My packages, Rcwl and RcwlPipelines got building error from the windows > machine. But those two packages have a BBSoption file to skip the windows > system and the packages didn't be checked in the tokay1 before. Could you > help to check it? > > Thanks, > Qiang > > From: Bioc-devel on behalf of Hu, Qiang > > Sent: Friday, April 26, 2019 2:47 PM > To: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple > platform build/check report for BioC 3.9 > > Hi all, > > > Could you please help to check whether the required python package "cwltool" > is installed and works in malbec2 and celaya2? > > Here is part of the error log in malbec2: > > $cwltool --version > > ... > > pkg_resources.DistributionNotFound: The 'pyparsing' distribution was not > found and is required by rdflib > ... > It seems the cwltool doesn't work properly. > > For elaya2, the required cwltool is not installed. > > > Thanks, > Qiang > > > > From: bbs-nore...@bioconductor.org > Sent: Friday, April 26, 2019 2:16:38 PM > To: Hu, Qiang > Subject: EXTERNAL: Rcwl problems reported in the Multiple platform > build/check report for BioC 3.9 > > [This is an automatically generated email. Please don't reply.] > > Hi Rcwl maintainer, > > According to the Multiple platform build/check report for BioC 3.9, > the Rcwl package has the following problem(s): > >o ERROR for 'R CMD INSTALL' on malbec2. See the details here: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dinstall.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=8jgPoOfCnzRwXCi7faEKLCkTzzcfbX8ywB_szlBJ1U4= > >o ERROR for 'R CMD build' on malbec2. See the details here: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=LXm1HJPGIDQVwrCOyV5oG6BT4ls6w07CEwQ7QsQly2o= > > Please take the time to address this by committing and pushing > changes to your package at git.bioconductor.org > > Notes: > >* This was the status of your package at the time this email was sent to > you. > Given that the online report is updated daily (in normal conditions) you > could see something different when you visit the URL(s) above, > especially if > you do so several days after you received this email. > >* It is possible that the problems reported in this report are false > positives, > either because another package (from CRAN or Bioconductor) breaks your > package (if yours depends on it) or because of a Build System problem. > If this is the case, then you can ignore this email. > >* Please check the report again 24h after you've committed your changes to > the > package and make sure that all the problems have gone. > >* If you have questions about this report or need help with the > maintenance of your package, please use the Bioc-devel mailing list: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_help_mailing-2Dlist_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=Cm8APMKdeEGzMe5TxCWrTshr83X4-n_dxeul4kDLiQM= > > (all package maintainers are requested to subscribe to this list) > > For immediate notification of package build status, please > subscribe to your package's RSS feed. Information is at: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_rss-2Dfeeds_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=NneDBUxDTN
Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9
Hi Qiang, Any reason why you use: UnsupportedPlatforms: win64, win32 and not just: UnsupportedPlatforms: win in your .BBSoptions file? Also make sure to have a line terminator: hpages@spectre:~/RcwlPipelines$ file .BBSoptions .BBSoptions: ASCII text, with no line terminators The lack of line terminator might be breaking the code that parses the file. Thanks, H. On 10/21/19 09:23, Hu, Qiang wrote: > Hi, > > My packages, Rcwl and RcwlPipelines got building error from the windows > machine. But those two packages have a BBSoption file to skip the windows > system and the packages didn't be checked in the tokay1 before. Could you > help to check it? > > Thanks, > Qiang > > From: Bioc-devel on behalf of Hu, Qiang > > Sent: Friday, April 26, 2019 2:47 PM > To: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple > platform build/check report for BioC 3.9 > > Hi all, > > > Could you please help to check whether the required python package "cwltool" > is installed and works in malbec2 and celaya2? > > Here is part of the error log in malbec2: > > $cwltool --version > > ... > > pkg_resources.DistributionNotFound: The 'pyparsing' distribution was not > found and is required by rdflib > ... > It seems the cwltool doesn't work properly. > > For elaya2, the required cwltool is not installed. > > > Thanks, > Qiang > > > > From: bbs-nore...@bioconductor.org > Sent: Friday, April 26, 2019 2:16:38 PM > To: Hu, Qiang > Subject: EXTERNAL: Rcwl problems reported in the Multiple platform > build/check report for BioC 3.9 > > [This is an automatically generated email. Please don't reply.] > > Hi Rcwl maintainer, > > According to the Multiple platform build/check report for BioC 3.9, > the Rcwl package has the following problem(s): > >o ERROR for 'R CMD INSTALL' on malbec2. See the details here: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dinstall.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=8jgPoOfCnzRwXCi7faEKLCkTzzcfbX8ywB_szlBJ1U4= > >o ERROR for 'R CMD build' on malbec2. See the details here: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=LXm1HJPGIDQVwrCOyV5oG6BT4ls6w07CEwQ7QsQly2o= > > Please take the time to address this by committing and pushing > changes to your package at git.bioconductor.org > > Notes: > >* This was the status of your package at the time this email was sent to > you. > Given that the online report is updated daily (in normal conditions) you > could see something different when you visit the URL(s) above, > especially if > you do so several days after you received this email. > >* It is possible that the problems reported in this report are false > positives, > either because another package (from CRAN or Bioconductor) breaks your > package (if yours depends on it) or because of a Build System problem. > If this is the case, then you can ignore this email. > >* Please check the report again 24h after you've committed your changes to > the > package and make sure that all the problems have gone. > >* If you have questions about this report or need help with the > maintenance of your package, please use the Bioc-devel mailing list: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_help_mailing-2Dlist_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=Cm8APMKdeEGzMe5TxCWrTshr83X4-n_dxeul4kDLiQM= > > (all package maintainers are requested to subscribe to this list) > > For immediate notification of package build status, please > subscribe to your package's RSS feed. Information is at: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_rss-2Dfeeds_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA=NneDBUxDTN44mjpTAGSiwSYj7gEHqHenJMrudgZC7Fk= > > Thanks for contributing to the Bioconductor project! > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > a
Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9
Hi, My packages, Rcwl and RcwlPipelines got building error from the windows machine. But those two packages have a BBSoption file to skip the windows system and the packages didn't be checked in the tokay1 before. Could you help to check it? Thanks, Qiang From: Bioc-devel on behalf of Hu, Qiang Sent: Friday, April 26, 2019 2:47 PM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9 Hi all, Could you please help to check whether the required python package "cwltool" is installed and works in malbec2 and celaya2? Here is part of the error log in malbec2: $cwltool --version ... pkg_resources.DistributionNotFound: The 'pyparsing' distribution was not found and is required by rdflib ... It seems the cwltool doesn't work properly. For elaya2, the required cwltool is not installed. Thanks, Qiang From: bbs-nore...@bioconductor.org Sent: Friday, April 26, 2019 2:16:38 PM To: Hu, Qiang Subject: EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9 [This is an automatically generated email. Please don't reply.] Hi Rcwl maintainer, According to the Multiple platform build/check report for BioC 3.9, the Rcwl package has the following problem(s): o ERROR for 'R CMD INSTALL' on malbec2. See the details here: https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/Rcwl/malbec2-install.html o ERROR for 'R CMD build' on malbec2. See the details here: https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/Rcwl/malbec2-buildsrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project! 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 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
Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9
Hi Qiang, On 4/26/19 11:47, Hu, Qiang wrote: > Hi all, > > > Could you please help to check whether the required python package "cwltool" > is installed and works in malbec2 and celaya2? > > Here is part of the error log in malbec2: > > $cwltool --version > > ... > > pkg_resources.DistributionNotFound: The 'pyparsing' distribution was not > found and is required by rdflib > ... > It seems the cwltool doesn't work properly. For some reason Python module pyparsing was missing on malbec2 (it should have gotten installed when we installed cwltool, not sure what happened). Anyway, I just installed it. > > For elaya2, the required cwltool is not installed. Just installed it on celaya2 too. For the Windows builder, I'll try later (can't do it now). Cheers, H. > > > Thanks, > Qiang > > > > From: bbs-nore...@bioconductor.org > Sent: Friday, April 26, 2019 2:16:38 PM > To: Hu, Qiang > Subject: EXTERNAL: Rcwl problems reported in the Multiple platform > build/check report for BioC 3.9 > > [This is an automatically generated email. Please don't reply.] > > Hi Rcwl maintainer, > > According to the Multiple platform build/check report for BioC 3.9, > the Rcwl package has the following problem(s): > >o ERROR for 'R CMD INSTALL' on malbec2. See the details here: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dinstall.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0=JMomHfgL3UKCZ1s1nDmPcv2DIDwJGCzj7R77CF0Wqw0= > >o ERROR for 'R CMD build' on malbec2. See the details here: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0=z2kUI4w3STNibEq8YRobwXncHRSwcz0Ez8jXTHjcJLI= > > Please take the time to address this by committing and pushing > changes to your package at git.bioconductor.org > > Notes: > >* This was the status of your package at the time this email was sent to > you. > Given that the online report is updated daily (in normal conditions) you > could see something different when you visit the URL(s) above, > especially if > you do so several days after you received this email. > >* It is possible that the problems reported in this report are false > positives, > either because another package (from CRAN or Bioconductor) breaks your > package (if yours depends on it) or because of a Build System problem. > If this is the case, then you can ignore this email. > >* Please check the report again 24h after you've committed your changes to > the > package and make sure that all the problems have gone. > >* If you have questions about this report or need help with the > maintenance of your package, please use the Bioc-devel mailing list: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_help_mailing-2Dlist_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0=oVwf_Gfjf2KotB0GBzkO8lrG9Vvy6eiUd3eppNth-SI= > > (all package maintainers are requested to subscribe to this list) > > For immediate notification of package build status, please > subscribe to your package's RSS feed. Information is at: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_rss-2Dfeeds_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0=4Lk46J_oqluBXVcoOOeBw-IyRCCeZC3-m-WV3fjaSYM= > > Thanks for contributing to the Bioconductor project! > > > > 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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0=bjc3DUMKrCQFuj2qKhULnAMx2m7VYA9s20WMgoIOyKA= -- 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)
Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9
Hi all, Could you please help to check whether the required python package "cwltool" is installed and works in malbec2 and celaya2? Here is part of the error log in malbec2: $cwltool --version ... pkg_resources.DistributionNotFound: The 'pyparsing' distribution was not found and is required by rdflib ... It seems the cwltool doesn't work properly. For elaya2, the required cwltool is not installed. Thanks, Qiang From: bbs-nore...@bioconductor.org Sent: Friday, April 26, 2019 2:16:38 PM To: Hu, Qiang Subject: EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9 [This is an automatically generated email. Please don't reply.] Hi Rcwl maintainer, According to the Multiple platform build/check report for BioC 3.9, the Rcwl package has the following problem(s): o ERROR for 'R CMD INSTALL' on malbec2. See the details here: https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/Rcwl/malbec2-install.html o ERROR for 'R CMD build' on malbec2. See the details here: https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/Rcwl/malbec2-buildsrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project! 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