BioC 2.9: CHECK report for snpMatrix on liverpool

Package: snpMatrix

Version: 1.17.2

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings snpMatrix_1.17.2.tar.gz

StartedAt: 2011-05-09 15:45:33 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:47:20 -0700 (Mon, 09 May 2011)

EllapsedTime: 106.7 seconds

RetCode: 0

Status: OK

CheckDir: snpMatrix.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/snpMatrix.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snpMatrix/DESCRIPTION' ... OK
* this is package 'snpMatrix' version '1.17.2'
* 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 installed package size ... NOTE
  installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data      6.4Mb
    doc       4.1Mb
    extdata   1.8Mb
* checking package directory ... OK
* checking for portable file names ... 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: Fst.Rd:28-30: Dropping empty section \references
* 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 'snpMatrix' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c adler32.c -o adler32.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c bind.c -o bind.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c compress.c -o compress.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c count_gt.c -o count_gt.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c covwin.c -o covwin.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c crc32.c -o crc32.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c deflate.c -o deflate.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c force_hom.c -o force_hom.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c fst.c -o fst.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c glm_test.c -o glm_test.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c glm_test_R.c -o glm_test_R.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c gzclose.c -o gzclose.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c gzlib.c -o gzlib.o
gzlib.c: In function 'gz_error':
gzlib.c:518:1: warning: visibility attribute not supported in this configuration; ignored
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c gzread.c -o gzread.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c gzwrite.c -o gzwrite.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c hash_index.c -o hash_index.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c hphase.c -o hphase.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c ibs.c -o ibs.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c imputation.c -o imputation.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c in.c -o in.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c infback.c -o infback.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c inffast.c -o inffast.o
inffast.c: In function 'inflate_fast':
inffast.c:324:1: warning: visibility attribute not supported in this configuration; ignored
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c inflate.c -o inflate.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c inftrees.c -o inftrees.o
inftrees.c: In function 'inflate_table':
inftrees.c:330:1: warning: visibility attribute not supported in this configuration; ignored
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c input.c -o input.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c invert.c -o invert.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c ld_with.c -o ld_with.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c mla.c -o mla.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c outdata.c -o outdata.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c pairwise_linkage.c -o pairwise_linkage.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c read_chiamo.c -o read_chiamo.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c read_hapmap.c -o read_hapmap.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c read_pedfile.c -o read_pedfile.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c read_signals.c -o read_signals.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c readbed.c -o readbed.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c readped.c -o readped.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c sdfpw.c -o sdfpw.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c single_snp_tests.c -o single_snp_tests.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c snp_summary.c -o snp_summary.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c snpmpy.c -o snpmpy.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c solve_cubic.c -o solve_cubic.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c solve_quadratic.c -o solve_quadratic.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c structure.c -o structure.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c switch.c -o switch.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c tdt.c -o tdt.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c trees.c -o trees.o
trees.c: In function '_tr_init':
trees.c:410:1: warning: visibility attribute not supported in this configuration; ignored
trees.c: In function '_tr_stored_block':
trees.c:883:1: warning: visibility attribute not supported in this configuration; ignored
trees.c: In function '_tr_align':
trees.c:919:1: warning: visibility attribute not supported in this configuration; ignored
trees.c: In function '_tr_flush_block':
trees.c:1020:1: warning: visibility attribute not supported in this configuration; ignored
trees.c: In function '_tr_tally':
trees.c:1071:1: warning: visibility attribute not supported in this configuration; ignored
trees.c: At top level:
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c uncompr.c -o uncompr.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c zutil.c -o zutil.o
zutil.c: In function 'zcalloc':
zutil.c:308:1: warning: visibility attribute not supported in this configuration; ignored
zutil.c: In function 'zcfree':
zutil.c:316:1: warning: visibility attribute not supported in this configuration; ignored
gcc -shared -s -static-libgcc -o snpMatrix.dll tmp.def 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 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 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/snpMatrix.Rcheck/snpMatrix/libs/i386
** 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 ...
*** tangling vignette sources ...
   'clustering-comparison-vignette.Rnw' 
   'imputation-vignette.Rnw' 
   'pca-vignette.Rnw' 
   'snpMatrix-vignette.Rnw' 
   'tdt-vignette.Rnw' 
** testing if installed package can be loaded

* DONE (snpMatrix)

name	user	system	elapsed
Fst	0.35	0.01	0.37
X.snp-class	0.10	0.00	0.09
X.snp.matrix-class	0.06	0.03	0.11
chi.squared	0.05	0.02	0.10
epsout.ld.snp	0.17	0.01	0.22
families	0.03	0.00	0.03
filter.rules	0	0	0
for.exercise	0.76	0.00	0.76
ibs.stats	0.13	0.02	0.14
ibsCount	0.20	0.01	0.22
ibsDist	0.13	0.04	0.16
imputation.maf	0	0	0
impute.snps	2.75	0.17	2.92
ld.snp	0.13	0.00	0.12
ld.with	0.09	0.01	0.11
misinherits	0.03	0.00	0.03
pair.result.ld.snp	0.05	0.00	0.05
plot.snp.dprime	0.25	0.00	0.25
pool	0.25	0.00	0.25
qq.chisq	0	0	0
read.HapMap.data	0	0	0
read.snps.chiamo	0	0	0
read.wtccc.signals	0	0	0
row.summary	0.13	0.00	0.12
single.snp.tests	0.07	0.00	0.08
snp-class	0	0	0
snp.cbind	0.33	0.14	0.49
snp.clust.plot	0.03	0.00	0.03
snp.compare	0.02	0.00	0.01
snp.cor	0.87	0.02	0.89
snp.dprime-class	0.07	0.00	0.07
snp.estimates.glm-class	0	0	0
snp.imputation	2.50	0.16	2.65
snp.lhs.estimates	0.39	0.03	0.42
snp.lhs.tests	0.11	0.01	0.21
snp.matrix-class	0.17	0.03	0.21
snp.pre.multiply	0.10	0.02	0.10
snp.reg.imputation-class	0	0	0
snp.rhs.estimates	0.09	0.00	0.10
snp.rhs.tests	0.05	0.02	0.06
snp.tests.glm-class	0	0	0
snp.tests.single-class	0	0	0
switch.alleles	0.08	0.01	0.09
tdt.snp	0.03	0.00	0.04
test.allele.switch	0.19	0.02	0.20
testdata	0.11	0.03	0.15
write.snp.matrix	7.37	0.28	7.98
xxt	0.82	0.00	0.81

Summary

Command output