Package: snpMatrix

Version: 1.12.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings snpMatrix_1.12.0.tar.gz

StartedAt: 2010-10-04 19:59:57 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 20:01:02 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 65.5 seconds

RetCode: 0

Status:  OK

CheckDir: snpMatrix.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/snpMatrix.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snpMatrix/DESCRIPTION' ... OK
* this is package 'snpMatrix' version '1.12.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'snpMatrix' can be installed ... OK
* 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: snp.clust.plot.Rd:34-36: Dropping empty section \note
prepare_Rd: snp.clust.plot.Rd:31-33: Dropping empty section \author
prepare_Rd: snp.clust.plot.Rd:28-30: Dropping empty section \references
prepare_Rd: snp.compare.Rd:36-38: Dropping empty section \note
prepare_Rd: snp.compare.Rd:33-35: Dropping empty section \author
prepare_Rd: snp.compare.Rd:30-32: Dropping empty section \references
prepare_Rd: snp.compare.Rd:42-44: Dropping empty section \seealso
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'snpMatrix' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c adler32.c -o adler32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c bind.c -o bind.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c compress.c -o compress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c count_gt.c -o count_gt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c covwin.c -o covwin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c crc32.c -o crc32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c deflate.c -o deflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c force_hom.c -o force_hom.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c glm_test.c -o glm_test.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c glm_test_R.c -o glm_test_R.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c gzio.c -o gzio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c hash_index.c -o hash_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c hphase.c -o hphase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ibs.c -o ibs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c imputation.c -o imputation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c in.c -o in.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c infback.c -o infback.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inffast.c -o inffast.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inflate.c -o inflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c inftrees.c -o inftrees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c input.c -o input.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c invert.c -o invert.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ld_with.c -o ld_with.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c mla.c -o mla.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c outdata.c -o outdata.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c pairwise_linkage.c -o pairwise_linkage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c read_chiamo.c -o read_chiamo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c read_hapmap.c -o read_hapmap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c read_pedfile.c -o read_pedfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c read_signals.c -o read_signals.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readbed.c -o readbed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readped.c -o readped.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c sdfpw.c -o sdfpw.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c single_snp_tests.c -o single_snp_tests.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c snp_summary.c -o snp_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c snpmpy.c -o snpmpy.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c solve_cubic.c -o solve_cubic.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c solve_quadratic.c -o solve_quadratic.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c structure.c -o structure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c switch.c -o switch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c tdt.c -o tdt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c trees.c -o trees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c uncompr.c -o uncompr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c zutil.c -o zutil.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o snpMatrix.so adler32.o bind.o compress.o count_gt.o covwin.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o hphase.o ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o invert.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readbed.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o switch.o tdt.o trees.o uncompr.o zutil.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/snpMatrix.Rcheck/snpMatrix/libs
** R
** data
** inst
** preparing package for lazy loading
Loading required package: splines
Creating a new generic function for "plot" in "snpMatrix"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (snpMatrix)

name	user	system	elapsed
X.snp-class	0.092	0.008	0.098
X.snp.matrix-class	0.240	0.012	0.252
chi.squared	0.120	0.004	0.124
epsout.ld.snp	0.176	0.008	0.185
families	0.036	0.000	0.036
filter.rules	0	0	0
for.exercise	1.228	0.012	1.240
ibs.stats	0.124	0.008	0.134
ibsCount	0.284	0.008	0.294
ibsDist	0.200	0.000	0.196
imputation.maf	0	0	0
impute.snps	4.676	0.124	4.803
ld.snp	0.100	0.004	0.101
ld.with	0.080	0.008	0.087
misinherits	0.028	0.004	0.033
pair.result.ld.snp	0.036	0.004	0.043
plot.snp.dprime	0.152	0.012	0.163
pool	0.168	0.004	0.171
qq.chisq	0	0	0
read.HapMap.data	0.000	0.000	0.001
read.snps.chiamo	0	0	0
read.wtccc.signals	0.000	0.000	0.001
row.summary	0.124	0.000	0.125
single.snp.tests	0.084	0.000	0.082
snp-class	0	0	0
snp.cbind	0.432	0.020	0.455
snp.clust.plot	0.024	0.000	0.027
snp.compare	0.012	0.004	0.016
snp.cor	0.816	0.000	0.834
snp.dprime-class	0.056	0.000	0.056
snp.estimates.glm-class	0.004	0.000	0.002
snp.imputation	4.532	0.024	4.557
snp.lhs.estimates	0.508	0.016	0.525
snp.lhs.tests	0.096	0.004	0.100
snp.matrix-class	0.284	0.008	0.291
snp.pre.multiply	0.084	0.000	0.084
snp.reg.imputation-class	0.004	0.000	0.001
snp.rhs.estimates	0.088	0.000	0.088
snp.rhs.tests	0.048	0.000	0.049
snp.tests.glm-class	0.000	0.000	0.001
snp.tests.single-class	0.000	0.004	0.003
switch.alleles	0.084	0.000	0.083
tdt.snp	0.028	0.000	0.027
test.allele.switch	0.209	0.000	0.206
testdata	0.16	0.00	0.16
xxt	0.712	0.000	0.713