* checking for file 'GGtools/DESCRIPTION' ... OK
* preparing 'GGtools':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'GGtools' ...
** libs
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -I/usr/local/include -fPIC -g -O2 -Wall -c minfra.cc -o minfra.o
minfra.cc: In function 'matrix operator/(matrix&, matrix&)':
minfra.cc:459: warning: unused variable 'a2c'
minfra.cc: In function 'matrix delete_col(matrix, int)':
minfra.cc:545: warning: unused variable 'ncop'
minfra.cc:545: warning: unused variable 'nresel'
minfra.cc:545: warning: unused variable 'skip'
minfra.cc:546: warning: unused variable 'resbase'
minfra.cc:546: warning: unused variable 'Xbase'
minfra.cc: In function 'int split(matrix&, matrix&, matrix*)':
minfra.cc:1210: warning: unused variable 'j'
minfra.cc: In function 'matrix* split(matrix&, matrix&)':
minfra.cc:1245: warning: unused variable 'j'
g++ -G -L/usr/local/lib -o GGtools.so minfra.o
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: hgfocus
Loading required package: geneplotter
Loading required package: annotate
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Creating a new generic function for "nrow" in "GGtools"
** help
>>> Building/Updating help pages for package 'GGtools'
Formats: text html latex example
HM2rac text html latex example
HMworkflow text html latex example
Strains2rac text html latex example
geneLocs text html latex example
genoStrings text html latex example
make_racExSet text html latex example
plot_EvG text html latex example
racExSet-class text html latex example
snpMeta-class text html latex example
snpScreen text html latex example
snps text html latex example
** building package indices ...
Loading required package: methods
* DONE (GGtools)
* creating vignettes ... ERROR
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: hgfocus
Loading required package: geneplotter
Loading required package: annotate
Loading required package: lattice
/loc/biocbuild/2.0d/R/bin/texi2dvi: pdflatex exited with bad status, quitting.
/loc/biocbuild/2.0d/R/bin/texi2dvi: see GGoverview.log for errors.
Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet = quiet) :
running texi2dvi on 'GGoverview.tex' failed
In addition: Warning message:
some genotype results had missing values; associated SNPs are dropped completely in this version when fastAGM is used. in: snpScreen(chr20GGdem, chr20meta, genesym("CPNE1"), ~., fastAGM,
Execution halted