Thank you for your concern. There is some conflict on our system that we will look into further. For now, you can ignore this ERROR on mac - the reviewer of your package is aware.
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 Aimin Yan <aimin.at.w...@gmail.com> Sent: Wednesday, September 27, 2017 12:49:13 PM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Something about time out errors I am submitting a R package to bioconductor. but I got the following warning and errors when I performed R CMD check. When I perform R CMD check on my local machines, it works. Is there a possible way that I can set up DISPLAY environment variable? Here is the link http://bioconductor.org/spb_reports/PathwaySplice_buildreport_20170925232327.html Thank you. Aimin OS X 10.11.6 El Capitan/x86_64 * checking R code for possible problems ... OK * checking Rd files ... WARNING gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL problem found in gmtGene2Cat.Rd * checking Rd metadata ... OK * checking files in vignettes ... WARNING Files in the 'vignettes' directory newer than all files in 'inst/doc': tutorial.html > # labeling each node by gene set name > enmap <- enrichmentMap(res,n=10,fixed = FALSE,similarity.threshold=0.3, + label.node.by.index = FALSE) Warning in fun(libname, pkgname) : no display name and no $DISPLAY environment variable Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : [tcl] invalid command name "font". Calls: enrichmentMap ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure Execution halted * checking for unstated dependencies in tests ... OK * checking tests ... Running testthat.R ERROR TIMEOUT: R CMD check exceeded 10mins linux (Ubuntu 16.04.1 LTS)/x86_64 * checking R code for possible problems ... OK * checking Rd files ... WARNING gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL problem found in gmtGene2Cat.Rd * checking Rd metadata ... OK * checking files in vignettes ... WARNING Files in the 'vignettes' directory newer than all files in 'inst/doc': tutorial.html > # labeling each node by gene set name > enmap <- enrichmentMap(res,n=10,fixed = FALSE,similarity.threshold=0.3, + label.node.by.index = FALSE) Warning in fun(libname, pkgname) : couldn't connect to display "localhost:10.0" Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : [tcl] invalid command name "font". Calls: enrichmentMap ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure Execution halted * checking for unstated dependencies in tests ... OK * checking tests ... Windows Server 2012 R2 Standard/x64 * checking R code for possible problems ... OK * checking Rd files ... WARNING gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL problem found in gmtGene2Cat.Rd * checking Rd metadata ... OK * checking files in vignettes ... WARNING Files in the 'vignettes' directory newer than all files in 'inst/doc': tutorial.html On Mon, Mar 27, 2017 at 12:22 PM, Aimin Yan <aimin.at.w...@gmail.com> wrote: > I am submitting a R package to bioconductor. but I got time out errors > when I performed R CMD check. > > > Is there a possible way that I can set up time to allow more time for R > CMD check? Or I have to use examples that they do not cost large time. > > > Thank you for your help > > Aimin > [[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
