Thanks Ashish for the quick fix. For the record the change to tidyr::gather() in the latest version of tidyr (v 1.0.0) also breaks the CNPBayes and SummarizedBenchmark packages:
https://bioconductor.org/checkResults/3.9/bioc-LATEST/CNPBayes/malbec2-buildsrc.html https://bioconductor.org/checkResults/3.9/bioc-LATEST/SummarizedBenchmark/malbec2-buildsrc.html Also FWIW the man page for gather() actually recommends to switch to pivot_longer(): Description: *Retired* Development on ‘gather()’ is complete, and for new code we recommend switching to ‘pivot_longer()’, which is easier to use, more featureful, and still under active development. ‘df %>% gather("key", "value", x, y, z)’ is equivalent to ‘df %>% pivot_longer(c(x, y, z), names_to = "key", values_to = "value")’ See more details in ‘vignette("pivot")’. Cheers, H. On 9/17/19 09:17, Ashish Jain wrote: > Hi Lori, > > Thank you for your help. I was able to reproduce the issue locally after > updating the packages. I updated the vignette with the changes and pushed > it on both RELEASE_3_9 and the development (3_10) branches. Again thank you > for your help! > > Regards, > Ashish Jain > > On Tue, Sep 17, 2019 at 7:06 AM Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > >> I am able to reproduce the ERROR. It seems to be an issue of trying to >> subset. >> >>> head(exp %>% gather(Tissue)) Tissue value >> 1 Adipose Tissue 1.63226821549951 >> 2 Adipose Tissue 0 >> 3 Adipose Tissue 0 >> 4 Adipose Tissue 0.485426827170242 >> 5 Adipose Tissue 0.584962500721156 >> 6 Adipose Tissue 3.05311133645956> head(exp %>% >> gather(Tissue=1:(ncol(exp)-1)))Error: 1 components of `...` had unexpected >> names. >> >> We detected these problematic arguments: >> * `Tissue` >> >> Did you misspecify an argument?Call `rlang::last_error()` to see a backtrace >> >>> >> >> You can see if there were any recent changes to package you depend on that >> could have caused this. A package you depend on may have changed their >> functionality. I needed to update packages (with BiocManager::install() >> update all ) in order to reproduce. >> >> Cheers, >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Cancer Institute >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> ------------------------------ >> *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ashish >> Jain <j...@iastate.edu> >> *Sent:* Monday, September 16, 2019 3:08 PM >> *To:* bioc-devel@r-project.org <bioc-devel@r-project.org> >> *Subject:* [Bioc-devel] Fwd: TissueEnrich problems reported in the >> Multiple platform build/check report for BioC 3.9 >> >> Hi All, >> >> I just got the message that my package is giving an error during the build >> process on Bioconductor build server. I saw the logs and found it is >> failing while building the vignette. I am not sure why it's happening as I >> have not updated the package since release and it was building without any >> errors. Can someone look into this? >> >> Regards, >> Ashish Jain >> >> ---------- Forwarded message --------- >> From: <bbs-nore...@bioconductor.org> >> Date: Mon, Sep 16, 2019 at 1:59 PM >> Subject: TissueEnrich problems reported in the Multiple platform >> build/check report for BioC 3.9 >> To: <j...@iastate.edu> >> >> >> [This is an automatically generated email. Please don't reply.] >> >> Hi TissueEnrich maintainer, >> >> According to the Multiple platform build/check report for BioC 3.9, >> the TissueEnrich package has the following problem(s): >> >> 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_TissueEnrich_malbec2-2Dbuildsrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=sA7mdXKmscGnnwrA2a-Dh9P7BpaJOuqIdbh1X6qTaAw&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=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=JXGAW15BKuxxLdjOHx8PlhDuRh-59gS7Cflq1M9BqCw&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=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=OjSaVg17RusRa0WJcDqfUcNQunuCqsiIaMD08K4cQBg&e= >> >> Thanks for contributing to the Bioconductor project! >> >> >> >> -- >> Regards, >> Ashish Jain >> Ph.D. Candidate >> Bioinformatics and Computational Biology >> Iowa State University >> Ph +1-317-529-7973 >> Website: >> *https://urldefense.proofpoint.com/v2/url?u=https-3A__ashishjain1988.github.io&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=EwM1zfwfJ7aRuNkay1qqCrf6BW291hXiN-1fbtIqWYY&e= >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__ashishjain1988.github.io_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=-nPXx1GhrMX43kHtc93JcC2fS8gKlNT9JuSqH4xJqUE&e= >> >/* >> >> [[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=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o1sr-o_MvUhGrSGKx6vufW6iDzp84bUofNfcGxAtObw&s=8BTASsfCqXyEE7tmClKkKeCbEBKmsOFx8tH2aKjKLtY&e= >> >> 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. > > > -- 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel