Package: chopsticks

Version: 1.17.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings chopsticks_1.17.1.tar.gz

StartedAt: 2011-05-09 11:59:33 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:00:53 -0700 (Mon, 09 May 2011)

EllapsedTime: 80.3 seconds

RetCode: 0

Status:  OK

CheckDir: chopsticks.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/chopsticks.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ version ‘1.17.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘chopsticks’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.9Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    data      6.4Mb
    doc       4.1Mb
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘chopsticks’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c adler32.c -o adler32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c bind.c -o bind.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c compress.c -o compress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c count_gt.c -o count_gt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c covwin.c -o covwin.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c crc32.c -o crc32.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c deflate.c -o deflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c force_hom.c -o force_hom.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c fst.c -o fst.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c glm_test.c -o glm_test.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c gzclose.c -o gzclose.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c gzlib.c -o gzlib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c gzread.c -o gzread.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c gzwrite.c -o gzwrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c hash_index.c -o hash_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c hphase.c -o hphase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ibs.c -o ibs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c imputation.c -o imputation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c in.c -o in.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c infback.c -o infback.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inffast.c -o inffast.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inflate.c -o inflate.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inftrees.c -o inftrees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c input.c -o input.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c invert.c -o invert.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ipf.c -o ipf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ld_with.c -o ld_with.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c misc.c -o misc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c mla.c -o mla.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c outdata.c -o outdata.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pairwise_linkage.c -o pairwise_linkage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c plink.c -o plink.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_chiamo.c -o read_chiamo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_hapmap.c -o read_hapmap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_pedfile.c -o read_pedfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_signals.c -o read_signals.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c read_uncertain.c -o read_uncertain.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readped.c -o readped.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c sdfpw.c -o sdfpw.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c snp_summary.c -o snp_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c solve_quadratic.c -o solve_quadratic.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c structure.c -o structure.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c switch.c -o switch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c tdt.c -o tdt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c trees.c -o trees.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c uncertain.c -o uncertain.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c uncompr.c -o uncompr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c zutil.c -o zutil.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o chopsticks.so adler32.o bind.o compress.o count_gt.o covwin.o crc32.o deflate.o force_hom.o fst.o glm_test.o glm_test_R.o gzclose.o gzlib.o gzread.o gzwrite.o hash_index.o hphase.o ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o invert.o ipf.o ld_graphic_eps.o ld_with.o misc.o mla.o outdata.o pairwise_linkage.o plink.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o read_uncertain.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 uncertain.o uncompr.o zutil.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/chopsticks.Rcheck/chopsticks/libs
** R
** data
** inst
** preparing package for lazy loading
Loading required package: splines
Creating a new generic function for "plot" in "chopsticks"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘chopsticks-vignette.Rnw’ 
   ‘clustering-comparison-vignette.Rnw’ 
   ‘imputation-vignette.Rnw’ 
   ‘pca-vignette.Rnw’ 
   ‘tdt-vignette.Rnw’ 
** testing if installed package can be loaded

* DONE (chopsticks)

name	user	system	elapsed
Fst	0.336	0.020	0.355
X.snp-class	0.120	0.020	0.139
X.snp.matrix-class	0.084	0.008	0.092
chi.squared	0.044	0.000	0.046
epsout.ld.snp	0.092	0.016	0.107
families	0.032	0.000	0.031
filter.rules	0.000	0.000	0.001
for.exercise	0.856	0.028	0.883
ibs.stats	0.132	0.000	0.131
ibsCount	0.240	0.000	0.242
ibsDist	0.148	0.000	0.158
imputation.maf	0.004	0.000	0.000
impute.snps	2.784	0.112	3.042
ld.snp	0.088	0.000	0.096
ld.with	0.072	0.008	0.085
misinherits	0.028	0.000	0.031
pair.result.ld.snp	0.040	0.000	0.042
plot.snp.dprime	0.152	0.008	0.166
plot.uncertainty	0	0	0
pool	0.160	0.000	0.172
qq.chisq	0	0	0
read.HapMap.data	0	0	0
read.beagle	0	0	0
read.impute	0	0	0
read.mach	0.084	0.008	0.099
read.snps.chiamo	0	0	0
read.wtccc.signals	0	0	0
row.summary	0.124	0.000	0.128
single.snp.tests	0.052	0.004	0.060
snp-class	0	0	0
snp.cbind	0.384	0.000	0.413
snp.clust.plot	0.024	0.004	0.026
snp.compare	0.012	0.004	0.020
snp.cor	0.812	0.004	0.849
snp.dprime-class	0.044	0.004	0.049
snp.estimates.glm-class	0.004	0.000	0.001
snp.imputation	2.496	0.096	2.592
snp.lhs.estimates	0.420	0.036	0.455
snp.lhs.tests	0.072	0.000	0.075
snp.matrix-class	0.184	0.004	0.189
snp.pre.multiply	0.072	0.008	0.077
snp.reg.imputation-class	0.000	0.000	0.001
snp.rhs.estimates	0.064	0.008	0.070
snp.rhs.tests	0.040	0.004	0.045
snp.tests.glm-class	0.000	0.000	0.001
snp.tests.single-class	0.004	0.000	0.002
switch.alleles	0.072	0.000	0.071
tdt.snp	0.020	0.004	0.023
test.allele.switch	0.140	0.004	0.145
testdata	0.120	0.000	0.122
write.plink	0.116	0.000	0.117
write.snp.matrix	3.020	0.220	3.245
xxt	0.800	0.020	0.818