[Bioc-devel] Vignette building fails

[Dan Tenenbaum]

Also be sure you are using a recent version of R-devel.
Dan


----- Original Message -----
> From: "Paul Grosu" <pgrosu at gmail.com>
> To: "Fan, Jean" <jeanfan at fas.harvard.edu>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Thursday, January 28, 2016 7:49:09 AM
> Subject: Re: [Bioc-devel] Vignette building fails

> Hi Jean,
> 
> I think you might need to update the required packages, so that they
> install if you don't have them installed.  The test I usually run is by
> keeping clean R installations and testing packages fresh as if I am a user
> who just downloaded R.  You seem to need org.Hs.eg.db and GO.db for the
> vignette, which I'm not sure the package automatically downloads, but those
> can take some time.
> 
> And as always feel free to check with folks on this list :)
> 
> Hope it helps,
> `p
> 
> On Thu, Jan 28, 2016 at 9:44 AM, Fan, Jean <jeanfan at fas.harvard.edu> wrote:
> 
>> Hi Martin,
>>
>> Ah, I didn’t realize the problems were connected. Yes, the vignettes do
>> take quite a while to run. I’ll see what I can do. Thanks for the help.
>>
>> Best,
>> Jean
>>
>> > On Jan 28, 2016, at 9:28 AM, Morgan, Martin <
>> Martin.Morgan at roswellpark.org> wrote:
>> >
>> > I tried to build your vignettes on my own computer, but they are taking
>> too long. From
>> >
>> >  http://bioconductor.org/developers/package-guidelines/#correctness
>> >
>> > the time limit for checking a package (which includes running the
>> vignette code, though not building the vignette) is 5 minutes. Do your
>> vignettes take a lot of time to build?
>> >
>> > If so, you should first identify the slow portion of your code and
>> attempt to vectorize it; ask here for help if needed.
>> >
>> > You should then construct examples for use in your vignette that are
>> sufficiently realistic to shine a favorable light on the full richness of
>> your software, but easily computed within the available time.
>> >
>> > Martin
>> >
>> > ________________________________________
>> > From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Fan,
>> Jean <jeanfan at fas.harvard.edu>
>> > Sent: Thursday, January 28, 2016 8:37 AM
>> > To: bioc-devel at r-project.org
>> > Subject: [Bioc-devel] Vignette building fails
>> >
>> > Hello,
>> >
>> > I recently updated my bioconductor package via svn. The package was
>> built successfully on my computer via R CMD build scde and passed R CMD
>> check scde and R CMD BiocCheck scde. But the build report on Bioconductor
>> ran into the following errors when building the vignettes:
>> >
>> > * checking for file ‘scde/DESCRIPTION’ ... OK
>> > * preparing ‘scde’:
>> > * checking DESCRIPTION meta-information ... OK
>> > * cleaning src
>> > * installing the package to build vignettes
>> > * creating vignettes ... ERROR
>> > Loading required package: flexmix
>> > Loading required package: lattice
>> > Error: processing vignette 'diffexp.Rmd' failed with diagnostics:
>> > Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’)
>> for vignette with name ‘diffexp’. The following files exist in directory
>> ‘.’: ‘diffexp.R’, ‘diffexp.Rmd’, ‘diffexp.md’, ‘pagoda.Rmd’
>> > Execution halted
>> >
>> > I was able to build the vignettes locally using R CMD Sweave so I’m not
>> sure what’s wrong. I haven’t been able to find any solutions by Googling
>> around. Has anyone else encountered this error before?
>> >
>> > Thanks,
>> > Jean
>> >
>> > Jean Fan
>> > PhD Candidate
>> > NSF GRFP
>> > Kharchenko Lab
>> > Harvard University
>> > 10 Shattuck St #3, Countway 336B
>> > Boston, MA 02115
>> >
>> >        [[alternative HTML version deleted]]
>> >
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