Re: [Bioc-devel] BiocCheck error
Martin,
Thank you. yes, you are right.
Now it works, I also changed outputs to tempfile() or tempdir().
Aimin
On Tue, Apr 10, 2018 at 6:07 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> Hi Aimin -- the problem is that your vignette has two VignetteEngine
> commands in it
>
> PathwaySplice/vignettes master$ grep VignetteEngine *
> tutorial.Rmd: %\VignetteEngine{knitr::rmarkdown}
> tutorial.Rmd: %\VignetteEngine{knitr::knitr}
>
> Also, please avoid writing to files in the user system, replace 'C:/temp'
> with tempfile() or dir = tempfile(); dir.create(dir) in code like the
> following
>
> PathwaySplice master$ grep -r "C:/" *
> man/runPathwaySplice.Rd: output.file='C:/temp/test.csv')
> man/runPathwaySplice.Rd: output.file='C:/temp/test.csv')
> man/enrichmentMap.Rd: label.node.by.index = TRUE,
> output.file.dir='C:/temp')
> man/enrichmentMap.Rd: label.node.by.index = FALSE,
> output.file.dir='C:/temp')}
> man/compareResults.Rd:compareResults(20, res.adj, res.unadj,
> gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
> R/Run_pathwaysplice.R:#' output.file='C:/temp/test.csv')
> R/Run_pathwaysplice.R:#' output.file='C:/temp/test.csv')
> R/Run_pathwaysplice.R:#' label.node.by.index = TRUE,
> output.file.dir='C:/temp')
> R/Run_pathwaysplice.R:#' label.node.by.index =
> FALSE, output.file.dir='C:/temp')}
> R/Run_pathwaysplice.R:#' compareResults(20, res.adj, res.unadj,
> gene.based.table, type.boxplot='Only3',output.dir='C:/TEMP')
>
> Martin
>
>
> On 04/10/2018 04:39 PM, Aimin Yan wrote:
>
>> I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed
>> without errors and warnings.
>>
>> However I get the following error when I use "R CMD BiocCheck
>> PathwaySplice_1.3.0.tar.gz"
>>
>> R CMD BiocCheck PathwaySplice_1.3.0.tar.gz
>>
>> This is BiocCheck version 1.15.8. BiocCheck is a work in progress.
>>
>> Output and severity of issues may change. Installing package...
>>
>> * Checking for version number mismatch...
>>
>> * Checking if other packages can import this one...
>>
>> * Checking to see if we understand object initialization...
>>
>> * NOTE: Consider clarifying how 12 object(s) are initialized. Maybe
>>
>>they are part of a data set loaded with data(), or perhaps part
>>
>>of an object referenced in with() or within().
>>
>> object (function)
>>
>>winMenuAddItem (.onAttach)
>>
>>ggplot (compareResults2)
>>
>>aes (compareResults2)
>>
>>random_sampling_200k (compareResults2)
>>
>>PValue (compareResults2)
>>
>>PathwaySplice (compareResults2)
>>
>>geom_point (compareResults2)
>>
>>geom_smooth (compareResults2)
>>
>>labs (compareResults2)
>>
>>scale_colour_manual (compareResults2)
>>
>>scale_shape_manual (compareResults2)
>>
>>get.col.scale (netplot)
>>
>> * Checking vignette directory...
>>
>> This is a software package
>>
>> Error in vapply(vigdircontents, vigHelper, logical(1), builder = desc) :
>>
>>values must be length 1,
>>
>> but FUN(X[[1]]) result is length 2
>>
>> Calls: ... BiocCheck -> checkVignetteDir -> checkVigBuilder ->
>> vapply
>>
>> Execution halted
>>
>>
>>
>> Any idea about this?
>>
>>
>> Here is my sessionInfo()
>>
>> https://gist.github.com/aiminy/764718da9b9eeedd6f5eea196ce956b4
>>
>> Thank you,
>>
>> Aimin
>>
>> [[alternative HTML version deleted]]
>>
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>> Bioc-devel@r-project.org mailing list
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>>
>>
>
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[Bioc-devel] BiocCheck error
I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed without errors and warnings. However I get the following error when I use "R CMD BiocCheck PathwaySplice_1.3.0.tar.gz" R CMD BiocCheck PathwaySplice_1.3.0.tar.gz This is BiocCheck version 1.15.8. BiocCheck is a work in progress. Output and severity of issues may change. Installing package... * Checking for version number mismatch... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 12 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). object (function) winMenuAddItem (.onAttach) ggplot (compareResults2) aes (compareResults2) random_sampling_200k (compareResults2) PValue (compareResults2) PathwaySplice (compareResults2) geom_point (compareResults2) geom_smooth (compareResults2) labs (compareResults2) scale_colour_manual (compareResults2) scale_shape_manual (compareResults2) get.col.scale (netplot) * Checking vignette directory... This is a software package Error in vapply(vigdircontents, vigHelper, logical(1), builder = desc) : values must be length 1, but FUN(X[[1]]) result is length 2 Calls: ... BiocCheck -> checkVignetteDir -> checkVigBuilder -> vapply Execution halted Any idea about this? Here is my sessionInfo() https://gist.github.com/aiminy/764718da9b9eeedd6f5eea196ce956b4 Thank you, Aimin [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 -> -> 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 -> -> 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
[Bioc-devel] warning on href
I got this warning when I perform CRAN check on my package
* checking Rd files ... WARNING
gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL
problem found in ‘gmtGene2Cat.Rd’
Here is my code for this Rd
@details This function reads a gene set file in \href{
https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29}{GMT
format}, and returns a list with its name being a gene id, and each element
of ...
I did not get this warning when I perform BiocCheck on my package.
Does anyone has an idea on how to fix this?
Thank you,
Aimin
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[Bioc-devel] Question about creating a bulleted list without bullets in rstudio
I have a question about making R package documentation.
I use rstudio to make this package. In my test.R file, I have code like the
following:
...
#' @return Returns a dataframe with several following variables (columns)
#' \itemize{
#' \item geneID: Gene ID
#' \item geneWisePvalue: each gene is represented by the smallest
p-value among its features
#' \item sig.gene: a gene is significant (1) or not (0)
#' \item mostSigDeFeature: the most significant gene feature
#' \item numFeature: number of gene features within the gene
#' }
...
After rebuild, I get help documentation like the following:
Value
Returns a dataframe with several following variables (columns)
-
geneID: Gene ID
-
geneWisePvalue: each gene is represented by the smallest p-value among
its features
-
sig.gene: a gene is significant (1) or not (0)
-
mostSigDeFeature: the most significant gene feature
-
numFeature: number of gene features within the gene
Now, I want to get the following:
Value
Returns a dataframe with several following variables (columns)
geneID: Gene ID
geneWisePvalue: each gene is represented by the smallest
p-value among its features
sig.gene: a gene is significant (1) or not (0)
mostSigDeFeature: the most significant gene feature
numFeature: number of gene features within the gene
That is to say, to create a a bulleted list without bullets.
Does anyone has idea on how to change settings in test.R file?
Thank you,
Aimin
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Re: [Bioc-devel] Check error on malbec2
Yes, it is. Aimin On Wed, Apr 5, 2017 at 7:20 AM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Are these permanent system files or files that are created during > examples/vignettes? > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Aimin Yan <aimin.at.w...@gmail.com> > *Sent:* Tuesday, April 4, 2017 3:41:02 PM > *To:* Shepherd, Lori > *Cc:* bioc-devel@r-project.org > *Subject:* Re: [Bioc-devel] Check error on malbec2 > > Thank you, I changed to use tempdir(), and it works now. > One more question is how to locate those outputs in temporary directory since > I want users to use those outputs. > > Aimin > > On Tue, Apr 4, 2017 at 2:00 PM, Shepherd, Lori < > lori.sheph...@roswellpark.org> wrote: > >> Write and access your output to a temporary directory instead using >> tempdir(). >> >> >> >> 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:* Tuesday, April 4, 2017 1:45:28 PM >> *To:* bioc-devel@r-project.org >> *Subject:* [Bioc-devel] Check error on malbec2 >> >> In the package I am trying ti submit to bioconductor, I got the following >> error for check. >> >> Warning in dir.create(output.file.dir) : >> cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission >> denied' >> Warning in file(file, ifelse(append, "a", "w")) : >> cannot open file '/home/pkgbuild/OutputEnmap/enrichmap_GO.xls': No such >> file or directory >> Error in file(file, ifelse(append, "a", "w")) : >> cannot open the connection >> Calls: enrichmentmap -> write.table -> file >> >> It seems I do not have permission to create a directory. >> Does anyone know how to fix this check error? >> >> >> Thanks, >> 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. > > > > 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
Re: [Bioc-devel] Check error on malbec2
Thank you, I changed to use tempdir(), and it works now. One more question is how to locate those outputs in temporary directory since I want users to use those outputs. Aimin On Tue, Apr 4, 2017 at 2:00 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Write and access your output to a temporary directory instead using > tempdir(). > > > > 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:* Tuesday, April 4, 2017 1:45:28 PM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] Check error on malbec2 > > In the package I am trying ti submit to bioconductor, I got the following > error for check. > > Warning in dir.create(output.file.dir) : > cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission > denied' > Warning in file(file, ifelse(append, "a", "w")) : > cannot open file '/home/pkgbuild/OutputEnmap/enrichmap_GO.xls': No such > file or directory > Error in file(file, ifelse(append, "a", "w")) : > cannot open the connection > Calls: enrichmentmap -> write.table -> file > > It seems I do not have permission to create a directory. > Does anyone know how to fix this check error? > > > Thanks, > 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
[Bioc-devel] Check error on malbec2
In the package I am trying ti submit to bioconductor, I got the following error for check. Warning in dir.create(output.file.dir) : cannot create dir '/home/pkgbuild/OutputEnmap', reason 'Permission denied' Warning in file(file, ifelse(append, "a", "w")) : cannot open file '/home/pkgbuild/OutputEnmap/enrichmap_GO.xls': No such file or directory Error in file(file, ifelse(append, "a", "w")) : cannot open the connection Calls: enrichmentmap -> write.table -> file It seems I do not have permission to create a directory. Does anyone know how to fix this check error? Thanks, Aimin [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Something about time out errors
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
[Bioc-devel] Question about using R-devel
When I used R-devel to perform R CMD build on my package, I got the following errors. Actually, I put ^packrat/ in PathwaySplice/.Rbuildignore. Does anyone has idea on this error? Thank you, Aimin cp: PathwaySplice/packrat/lib-R/boot: No such file or directory cp: PathwaySplice/packrat/lib-R/class: No such file or directory cp: PathwaySplice/packrat/lib-R/codetools: No such file or directory cp: PathwaySplice/packrat/lib-R/compiler: No such file or directory cp: PathwaySplice/packrat/lib-R/datasets: No such file or directory cp: PathwaySplice/packrat/lib-R/graphics: No such file or directory cp: PathwaySplice/packrat/lib-R/grDevices: No such file or directory cp: PathwaySplice/packrat/lib-R/grid: No such file or directory cp: PathwaySplice/packrat/lib-R/KernSmooth: No such file or directory cp: PathwaySplice/packrat/lib-R/MASS: No such file or directory cp: PathwaySplice/packrat/lib-R/methods: No such file or directory cp: PathwaySplice/packrat/lib-R/nnet: No such file or directory cp: PathwaySplice/packrat/lib-R/parallel: No such file or directory cp: PathwaySplice/packrat/lib-R/rpart: No such file or directory cp: PathwaySplice/packrat/lib-R/spatial: No such file or directory cp: PathwaySplice/packrat/lib-R/splines: No such file or directory cp: PathwaySplice/packrat/lib-R/stats: No such file or directory cp: PathwaySplice/packrat/lib-R/stats4: No such file or directory cp: PathwaySplice/packrat/lib-R/tcltk: No such file or directory cp: PathwaySplice/packrat/lib-R/tools: No such file or directory cp: PathwaySplice/packrat/lib-R/utils: No such file or directory ERROR copying to build directory failed Error: Command failed (1) In addition: Warning message: `cleanup` is deprecated Execution halted [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
