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: [email protected] <[email protected]> > 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0&s=JMomHfgL3UKCZ1s1nDmPcv2DIDwJGCzj7R77CF0Wqw0&e= > > 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0&s=z2kUI4w3STNibEq8YRobwXncHRSwcz0Ez8jXTHjcJLI&e= > > 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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0&s=oVwf_Gfjf2KotB0GBzkO8lrG9Vvy6eiUd3eppNth-SI&e= > > (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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0&s=4Lk46J_oqluBXVcoOOeBw-IyRCCeZC3-m-WV3fjaSYM&e= > > 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]] > > _______________________________________________ > [email protected] mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qNOPA5kSx8Kv4dUadIB84x7JFi9_wqi0mahqhr4nck0&s=bjc3DUMKrCQFuj2qKhULnAMx2m7VYA9s20WMgoIOyKA&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: [email protected] Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
