* 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
** arch - i386
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -fPIC -g -O2 -march=pentium-m -mtune=prescott -c minfra.cc -o minfra.o
/var/tmp//cczFEHy5.s:20229:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20244:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20259:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20278:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20293:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20308:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20323:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20338:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20357:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20372:indirect jmp without `*'
/var/tmp//cczFEHy5.s:20387:indirect jmp without `*'
g++-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GGtools.so minfra.o -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c minfra.cc -o minfra.o
g++-4.0 -arch ppc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GGtools.so minfra.o -F/Library/Frameworks/R.framework/.. -framework R
** 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
/Library/Frameworks/R.framework/Resources/bin/texi2dvi: pdflatex exited with bad status, quitting.
/Library/Frameworks/R.framework/Resources/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