[Bioc-devel] Latex errors in R CMD check a new built BSgenome data package in R-2.13.0
Mao Jianfeng
jianfeng.mao at gmail.com
Thu Mar 31 09:35:21 CEST 2011
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
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