* checking for file 'GGtools/DESCRIPTION' ... OK
* preparing 'GGtools':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
installing R.css in E:/biocbld/2.0d/tmpdir/Rinst46896600
---------- Making package GGtools ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making minfra.d from minfra.cc
g++ -Ie:/biocbld/2.0d/R/include -Wall -O2 -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'
windres --include-dir e:/biocbld/2.0d/R/include -i GGtools_res.rc -o GGtools_res.o
g++ -shared -s -o GGtools.dll GGtools.def minfra.o GGtools_res.o -Le:/biocbld/2.0d/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
installing man source files
installing indices
Loading required package: methods
not zipping data
installing help
>>> Building/Updating help pages for package 'GGtools'
Formats: text html latex example chm
HM2rac text html latex example chm
HMworkflow text html latex example chm
Strains2rac text html latex example chm
geneLocs text html latex example chm
genoStrings text html latex example chm
make_racExSet text html latex example chm
plot_EvG text html latex example chm
racExSet-class text html latex example chm
snpMeta-class text html latex example chm
snpScreen text html latex example chm
snps text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\2.0d\Rpacks\GGtools\chm\GGtools.chm
Compile time: 0 minutes, 0 seconds
12 Topics
100 Local links
0 Internet links
1 Graphic
Created e:\biocbld\2.0d\Rpacks\GGtools\chm\GGtools.chm, 36,804 bytes
Compression decreased file by 32,821 bytes.
preparing package GGtools 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
Creating a new generic function for "nrow" in "GGtools"
adding MD5 sums
* 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
entering extended mode
E:/biocbld/2.0d/Rpacks/GGtools/inst/doc/GGoverview.tex:406: Missing $ inserted
E:/biocbld/2.0d/Rpacks/GGtools/inst/doc/GGoverview.tex:406: Extra }, or forgott
en
E:/biocbld/2.0d/Rpacks/GGtools/inst/doc/GGoverview.tex:412: Missing $ insertedtexify: pdflatex failed for some reason (see log file).
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