[Bioc-devel] vignette problems

Martin Morgan martin.morgan at roswellpark.org
Fri Mar 30 15:56:48 CEST 2018

On 03/29/2018 01:07 PM, campos wrote:
> Dear bioc-devel team,
> I have made some changes in the package STAN and although it seems to 
> install correctly, I have problems with timeout and error in windows... 
> Could someone help me to improve the time?
> https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/

it looks like, with your most recent commit (at the top of the page, 
'Snapshot Date', 'Last Commit', 'Last Changed Date'), the package built 
on Windows and Linux.

There is a segfault on Mac, which is likely a programming error in your 
C code. It could be debugged perhaps using valgrind or similar tools, 
but the first step would be to isolate the code to something more easily 
reproduced than the full vignette. It would also help to clean up the C 
code so that it compiles without warnings with the -Wall -pedantic flags


> Best,
> Rafael
> On 28.03.2018 01:08, Martin Morgan wrote:
>> When I try and install the version on the master branch of the 
>> Bioconductor git repository I get
>> STAN master$ Rdev --vanilla CMD INSTALL .
>> * installing to library ‘/home/mtmorgan/R/x86_64-pc-linux-gnu-library
>> ...
>> ** testing if installed package can be loaded
>> Error: package or namespace load failed for 'STAN' in 
>> namespaceExport(ns, exports):
>>  undefined exports: viterbi2Gviz
>> This comes about in a rather interesting way because the body of 
>> plotViterbi is not defined
>> plotViterbi <- function(viterbi, regions, gen, chrom, from, to, 
>> statecols, col)
>> #'
>> ...
>> Can you please commit a version of the package that installs?
>> Martin
>> On 03/27/2018 06:42 PM, campos wrote:
>>> Dear bioc-devel team,
>>> I am developing the STAN packages and I am running into problems when 
>>> trying to build my package. The problem is the following:
>>> Error in vignette_type(Outfile) :
>>>    Vignette product 'STAN.tex' does not have a known filename 
>>> extension ('NA')
>>> ERROR: installing vignettes failed
>>> * removing '/tmp/Rtmp925Iru/Rinst63471ff1efdc/STAN'
>>> I tried to build the package in old versions (which they used to 
>>> work) and I run in other problems but in this case is:
>>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = 
>>> quiet,  :
>>>    Running 'texi2dvi' on 'STAN.tex' failed.
>>> LaTeX errors:
>>> ! LaTeX Error: File `beramono.sty' not found.
>>> Type X to quit or <RETURN> to proceed,
>>> or enter new name. (Default extension: sty)
>>> Could you help me with this problem?
>>> Thank you very much,
>>> Rafael
>>> _______________________________________________
>>> Bioc-devel at 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...{{dropped:2}}

More information about the Bioc-devel mailing list