[Bioc-devel] Latex errors in R CMD check a new built BSgenome data package in R-2.13.0
Hervé Pagès
hpages at fhcrc.org
Thu Mar 31 22:44:51 CEST 2011
Hi Jian-Feng,
I'm not sure what's going on. I just re-forged
BSgenome.Athaliana.TAIR.TAIR9 with R 2.13 alpha, made the
source tarball with 'R CMD build', and then run 'R CMD check'
on this source tarball, and was not able to reproduce this.
I opened the manual (BSgenome.Athaliana.TAIR.TAIR9-manual.pdf,
located in BSgenome.Athaliana.TAIR.TAIR9.Rcheck) with acroread
and it looked OK.
I'm on an openSUSE 11.1 machine and have a standard texlive
installation. I'm not sure this is helpful to you but just in
case here is the list of texlive RPMs currently installed on
that machine:
hpages at merlot2:~> rpm -qa | grep -i texlive
texlive-bin-devel-2007-219.4
texlive-bin-musictex-2007-219.4
texlive-xmltex-2007-219.7.1
texlive-bin-metapost-2007-219.4
texlive-latex-2007-219.7.1
texlive-bin-jadetex-2007-219.4
texlive-jadetex-2007-219.7.1
texlive-bin-xmltex-2007-219.4
texlive-musictex-2007-219.7.1
texlive-bin-2007-219.7.1
texlive-bin-latex-2007-219.4
texlive-2007-219.7.1
texlive-metapost-2007-219.7.1
texlive-tools-2007-219.7.1
texlive-bin-tools-2007-219.4
A rather old texlive version as you can see. I'm going to try this
again on a server with openSUSE 11.3 where texlive is more recent
(2009).
You could try to produce the manual directly with:
R CMD Rd2pdf --batch --no-preview --no-clean BSgenome.Alyrata.JGI.v1/
I think this is how 'R CMD check' produces it so the above command
should fail with the same errors. Note that those errors are LaTeX
errors, so you could replace 'R CMD Rd2pdf' with 'R CMD Rd2dvi' in
the above command (keep all the options) and should still get the
same LaTeX errors.
The above command creates a folder named something like .Rd2dvi28311/
where intermediate files are dumped. Note that this is a hidden folder
so you need to use 'ls -a' to see it. One of the intermediate files
should be named Rd2.tex, and, in your case, is apparently not a valid
LaTeX file. If you run latex directly on it, again you should see the
same errors as previously.
It might help to look at this Rd2.tex file (you could show it to us,
just copy/paste it in your email).
Thanks,
H.
On 03/31/2011 12:35 AM, Mao Jianfeng wrote:
> Dear listers,
>
> Under helps from this mailing list, I have gotten my BSgenome data
> package built in R-2.13.0. Though it can be installed and loaded, the
> "R CMD check" returned me LaTex errors. I do not know how to deal with
> these errors.
>
> I hope to get more helps/directions from you. Thanks in advance.
>
> Best,
>
> Jian-Feng, Mao
>
>
> Here I show you the Info:
>
> (1) checking the package
> #################################################################
> jmao at deimos:~/Aly_test$ /ebio/abt6/jmao/bin/R-2.13/R-alpha/bin/R CMD
> check BSgenome.Alyrata.JGI.v1_1.0.tar.gz
> * using log directory ‘/ebio/abt6/jmao/Aly_test/BSgenome.Alyrata.JGI.v1.Rcheck’
> * using R version 2.13.0 alpha (2011-03-27 r55091)
> * using platform: x86_64-unknown-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ‘BSgenome.Alyrata.JGI.v1/DESCRIPTION’ ... OK
> * this is package ‘BSgenome.Alyrata.JGI.v1’ version ‘1.0’
> * checking package name space information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking for executable files ... OK
> * checking whether package ‘BSgenome.Alyrata.JGI.v1’ can be installed ... OK
> * checking installed package size ... NOTE
> installed size is 53.7Mb
> sub-directories of 1Mb or more:
> extdata 53.6Mb
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ... OK
> * checking whether the package can be unloaded cleanly ... OK
> * checking whether the name space can be loaded with stated dependencies ... OK
> * checking whether the name space can be unloaded cleanly ... OK
> * checking for unstated dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... NOTE
> prepare_Rd: package.Rd:15-17: Dropping empty section \details
> * checking Rd metadata ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking Rd contents ... OK
> * checking for unstated dependencies in examples ... OK
> * checking examples ... OK
> * checking PDF version of manual ... WARNING
> LaTeX errors when creating PDF version.
> This typically indicates Rd problems.
> LaTeX errors found:
> ! Font T1/ptm/m/n/10=ptmr8t at 10.0pt not loadable: Metric (TFM) file not found
> .
> <to be read again>
> relax
> l.7 \begin{document}
> ! Font T1/ptm/m/n/24.88=ptmr8t at 24.88pt not loadable: Metric (TFM) file not f
> ound.
> <to be read again>
> relax
> l.8 \chapter*{}
> ! Font T1/ptm/bx/n/24.88=ptmb8t at 24.88pt not loadable: Metric (TFM) file not
> found.
> <to be read again>
> relax
> l.8 \chapter*{}
> ! Font \T1/ptm/b/n/24.88=nullfont not loadable: Metric (TFM) file not found.
> <to be read again>
> \relax
> l.8 \chapter*{}
>
> ! Font T1/ptm/bx/n/10=ptmb8t at 10.0pt not loadable: Metric (TFM) file not foun
> d.
> <to be read again>
> relax
> l.10 ...f{\huge Package `BSgenome.Alyrata.JGI.v1'}
> ! Font \T1/ptm/b/n/10=nullfont not loadable: Metric (TFM) file not found.
> <to be read again>
> \relax
> l.10 ...f{\huge Package `BSgenome.Alyrata.JGI.v1'}
> }
> ! Font T1/ptm/bx/n/20.74=ptmb8t at 20.74pt not loadable: Metric (TFM) file not
> found.
> <to be read again>
> relax
> l.10 ...f{\huge Package `BSgenome.Alyrata.JGI.v1'}
> ! Font \T1/ptm/b/n/20.74=nullfont not loadable: Metric (TFM) file not found.
> <to be read again>
> \relax
> l.10 ...f{\huge Package `BSgenome.Alyrata.JGI.v1'}
> }
> ! Font T1/ptm/m/n/12=ptmr8t at 12.0pt not loadable: Metric (TFM) file not found
> .
> <to be read again>
> relax
> l.11 \par\bigskip{\large
> ! Font T1/pcr/m/n/10=pcrr8t at 10.0pt not loadable: Metric (TFM) file not found
> .
> <to be read again>
> relax
> l.22 ...n-Feng Mao }\email{jianfeng.mao at gmail.com}
> ! Font T1/ptm/m/n/14.4=ptmr8t at 14.4pt not loadable: Metric (TFM) file not fou
> nd.
> <to be read again>
> relax
> l.38 ...a full genome (JGI version V1.0)}{Alyrata}
> ! Font T1/ptm/bx/n/14.4=ptmb8t at 14.4pt not loadable: Metric (TFM) file not fo
> und.
> <to be read again>
> relax
> l.38 ...a full genome (JGI version V1.0)}{Alyrata}
> ! Font \T1/ptm/b/n/14.4=nullfont not loadable: Metric (TFM) file not found.
> <to be read again>
> \relax
> l.38 ...a full genome (JGI version V1.0)}{Alyrata}
>
> ! Font T1/phv/m/n/14.4=phvr8t at 14.4pt not loadable: Metric (TFM) file not fou
> nd.
> <to be read again>
> relax
> l.38 ...a full genome (JGI version V1.0)}{Alyrata}
> ! Font T1/ptm/m/it/10=ptmri8t at 10.0pt not loadable: Metric (TFM) file not fou
> nd.
> <to be read again>
> relax
> l.38 ...a full genome (JGI version V1.0)}{Alyrata}
> ! Font T1/ptm/m/n/9=ptmr8t at 9.0pt not loadable: Metric (TFM) file not found.
> <to be read again>
> relax
> l.76 \begin{ExampleCode}
>
> ! Font T1/pcr/m/n/9=pcrr8t at 9.0pt not loadable: Metric (TFM) file not found.
> <to be read again>
> relax
> l.76 \begin{ExampleCode}
>
> ! Font T1/ptm/m/sl/10=ptmro8t at 10.0pt not loadable: Metric (TFM) file not fou
> nd.
> <to be read again>
> relax
> l.108 if (interactive())
> ! Font T1/phv/m/n/10=phvr8t at 10.0pt not loadable: Metric (TFM) file not found
> .
> <to be read again>
> relax
> l.108 if (interactive())
> * checking PDF version of manual without hyperrefs or index ... ERROR
>
>
> (2) install the package
> #################################################################
>
> jmao at deimos:~/Aly_test$ /ebio/abt6/jmao/bin/R-2.13/R-alpha/bin/R CMD
> INSTALL BSgenome.Alyrata.JGI.v1_1.0.tar.gz
> * installing to library ‘/ebio/abt6/jmao/bin/R-2.13/Rpacks’
> * installing *source* package ‘BSgenome.Alyrata.JGI.v1’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
> pmin, pmin.int, rbind, rep.int, setdiff, table, union
>
> Loading required package: GenomicRanges
> Loading required package: Biostrings
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
>
> * DONE (BSgenome.Alyrata.JGI.v1)
>
> (3) loading the package
> #################################################################
>> library(BSgenome.Alyrata.JGI.v1)
> Loading required package: BSgenome
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
> pmin, pmin.int, rbind, rep.int, setdiff, table, union
>
> Loading required package: GenomicRanges
> Loading required package: Biostrings
>
>> seqlengths(Alyrata)
> chr1 chr2 chr3 chr4
> 33132539 19320864 24464547 23328337
> chr5 chr6 chr7 chr8
> 21221946 25113588 24649197 22951293
> chrM chrC_scaffold_373 chrC_scaffold_546 chrC_scaffold_732
> 214459 8873 6162 4750
> chrC_scaffold_757 chrC_scaffold_764 chrC_scaffold_885
> 4636 4615 4166
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
More information about the Bioc-devel
mailing list