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.work at 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