Hi,
I'm trying to submit a new package to Bioc. Using the automated package
builder, two out of three machines did not finish nicely. More specific, my
package passed Linux but failed Windows and Mac.
Here is the error messages for Windows:
================================
* checking for file 'GeneOverlap/DESCRIPTION' ... OK
* preparing 'GeneOverlap':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning: running command '"C:\PROGRA~2\MIKTEX~1.9\miktex\bin\texi2dvi.exe"
--quiet --pdf "GeneOverlap.tex" -I
"E:/packagebuilder/R/share/texmf/tex/latex" -I
"E:/packagebuilder/R/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave')
for vignette with name 'GeneOverlap'. The following files exists in
directory '.': 'GeneOverlap-013.pdf', 'GeneOverlap-019.pdf',
'GeneOverlap-020.pdf', 'GeneOverlap-concordance.tex', 'GeneOverlap.Rnw',
'GeneOverlap.bib', 'GeneOverlap.synctex.gz', 'GeneOverlap.tex', 'Rplots.pdf'
Calls: <Anonymous> -> find_vignette_product
Execution halted
It looks like the PDF file was not built but can it be more specific what
is wrong with the TEX file? How can I proceed from here?
Here is the error messages for Mac:
===========================
* checking for file 'GeneOverlap/DESCRIPTION' ... OK
* preparing 'GeneOverlap':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'GeneOverlap.tex' failed.
BibTeX errors:
The top-level auxiliary file: GeneOverlap.aux
The style file:
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BiocStyle/sty/unsrturl.bst
Illegal, another \bibstyle command---line 31 of file GeneOverlap.aux
: \bibstyle
: {apalike}
I'm skipping whatever remains of this command
Reallocated glb_str_ptr (elt_size=4) to 20 items from 10.
Reallocated global_strs (elt_size=20001) to 20 items from 10.
Reallocated glb_str_end (elt_size=4) to 20 items from 10.
Reallocated singl_function (elt_size=4) to 100 items from 50.
Database file #1: GeneOverlap.bib
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
I'm using the new BiocStyle package for vignette styling. However, the
package builder declared that one of its style files was illegal.
Both error messages are confusing and there is a lack of specifics for me
to diagnose what went wrong. Does anybody have similar experience?
Thanks,
--
Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
#################
Want ChIP-seq differential analysis? Use:
https://code.google.com/p/diffreps/
Test biological hypotheses with NGS data: https://code.google.com/p/ngsplot/
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