[Bioc-devel] Error from rmarkdown
Hi all, I am the maintainer of anamiR. I keep getting this error on build report, which I don't get it on my local environment. Also, the weird part is that it did not show up until this September. Does anyone how to fix this? it looks like something went wrong with t.test from stats, and I don't think this package has been changed... Quitting from lines 187-198 (IntroductionToanamiR.Rmd) Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics: not enough 'x' observations --- failed re-building ‘IntroductionToanamiR.Rmd’ Any suggestion would be helpful, Thank you! Ti-Tai ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] package named spdeq causes error
Hi all, I got an error about this... * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘anamiR’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called ‘spdep’ ERROR: lazy loading failed for package ‘anamiR’ * removing ‘/home/biocbuild/bbs-3.8-bioc/R/library/anamiR’ * restoring previous ‘/home/biocbuild/bbs-3.8-bioc/R/library/anamiR’ which I don't include package named 'spdeq' in my package... Anyone got this as well? Thanks, Ti-Tai ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] The warning about 'biocLite()'
Ok, Thank you very much. Best, Ti Tai 引述 "Shepherd, Lori" : Your package does look clean for BiocInstaller/biocLite - looking at the dependency I think this is coming from when your package is Installed and from the dependency gage that has not been updated yet. I think you can safely ignore this warning and when gage is updated it should automatically disappear. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: r04945...@ntu.edu.tw Sent: Monday, August 27, 2018 3:27:39 AM To: Shepherd, Lori Cc: bioc-devel Subject: Re: [Bioc-devel] The warning about 'biocLite()' Hi, It's anamiR. Best, Ti Tai Wang 引述 "Shepherd, Lori" : What is the name of your package? It is possible it could be coming from one of the packages you depend or import. If you are sure you replaced all the instances in your package this could be the case. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of r04945...@ntu.edu.tw Sent: Sunday, August 26, 2018 4:26:05 PM To: bioc-devel Subject: [Bioc-devel] The warning about 'biocLite()' Hi, I have already use 'BiocManager' to replace every 'biocLite' in my code, like vignette and README, but I still got "Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN" in my report. Any suggestion? Best, Ti Tai ___ 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. 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] The warning about 'biocLite()'
Hi, It's anamiR. Best, Ti Tai Wang 引述 "Shepherd, Lori" : What is the name of your package? It is possible it could be coming from one of the packages you depend or import. If you are sure you replaced all the instances in your package this could be the case. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of r04945...@ntu.edu.tw Sent: Sunday, August 26, 2018 4:26:05 PM To: bioc-devel Subject: [Bioc-devel] The warning about 'biocLite()' Hi, I have already use 'BiocManager' to replace every 'biocLite' in my code, like vignette and README, but I still got "Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN" in my report. Any suggestion? Best, Ti Tai ___ 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] The warning about 'biocLite()'
Hi, I have already use 'BiocManager' to replace every 'biocLite' in my code, like vignette and README, but I still got "Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN" in my report. Any suggestion? Best, Ti Tai ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
