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Package 468/517HostnameOS / ArchBUILDCHECKBUILD BIN
snpMatrix 1.18.0
David Clayton
Snapshot Date: 2011-11-14 18:21:56 -0800 (Mon, 14 Nov 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/snpMatrix
Last Changed Rev: 60265 / Revision: 60306
Last Changed Date: 2011-11-11 23:09:14 -0800 (Fri, 11 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: snpMatrix
Version: 1.18.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch snpMatrix_1.18.0.tar.gz
StartedAt: 2011-11-15 04:54:10 -0800 (Tue, 15 Nov 2011)
EndedAt: 2011-11-15 04:57:23 -0800 (Tue, 15 Nov 2011)
EllapsedTime: 193.6 seconds
RetCode: 0
Status:  OK  
CheckDir: snpMatrix.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/snpMatrix.Rcheck'
* using R version 2.14.0 (2011-10-31)
* 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 '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'snpMatrix' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data      6.4Mb
    doc       1.7Mb
    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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                            old_size new_size compress
  Genotypes.GenTrain1.RData     39Kb     30Kb       xz
  Genotypes.GenTrain2.RData     37Kb     29Kb       xz
  families.RData                46Kb     26Kb       xz
  for.exercise.RData           5.4Mb    3.5Mb       xz
  testdata.RData               880Kb    556Kb       xz
* 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 compiled code ... 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

snpMatrix.Rcheck/00install.out:

* installing *source* package 'snpMatrix' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c adler32.c -o adler32.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c bind.c -o bind.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c compress.c -o compress.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c count_gt.c -o count_gt.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c covwin.c -o covwin.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c crc32.c -o crc32.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c deflate.c -o deflate.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c force_hom.c -o force_hom.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c fst.c -o fst.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c glm_test.c -o glm_test.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_lhs_score':
glm_test_R.c:176:24: warning: unused variable 'Vnames'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c gzclose.c -o gzclose.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2 -c gzread.c -o gzread.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c gzwrite.c -o gzwrite.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c hash_index.c -o hash_index.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c hphase.c -o hphase.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c ibs.c -o ibs.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c imputation.c -o imputation.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c in.c -o in.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c infback.c -o infback.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2 -c inflate.c -o inflate.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2 -c input.c -o input.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c invert.c -o invert.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2 -c ld_with.c -o ld_with.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c mla.c -o mla.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c outdata.c -o outdata.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c pairwise_linkage.c -o pairwise_linkage.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c read_chiamo.c -o read_chiamo.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c read_hapmap.c -o read_hapmap.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c read_pedfile.c -o read_pedfile.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c read_signals.c -o read_signals.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c readbed.c -o readbed.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c readped.c -o readped.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c sdfpw.c -o sdfpw.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2 -c snp_summary.c -o snp_summary.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c snpmpy.c -o snpmpy.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c solve_cubic.c -o solve_cubic.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c solve_quadratic.c -o solve_quadratic.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c structure.c -o structure.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c switch.c -o switch.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -c tdt.c -o tdt.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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 -mtune=core2 -c uncompr.c -o uncompr.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -mtune=core2 -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
Creating a generic function for 'plot' from package 'graphics' in package '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)

snpMatrix.Rcheck/snpMatrix-Ex.timings:

nameusersystemelapsed
Fst0.350.030.38
X.snp-class0.090.030.12
X.snp.matrix-class0.090.000.10
chi.squared0.050.020.09
epsout.ld.snp0.160.020.19
families0.030.000.03
filter.rules000
for.exercise0.780.010.83
ibs.stats0.120.000.12
ibsCount0.210.000.24
ibsDist0.140.000.14
imputation.maf000
impute.snps2.640.162.83
ld.snp0.110.010.12
ld.with0.010.070.08
misinherits0.050.010.06
pair.result.ld.snp0.050.000.05
plot.snp.dprime0.180.020.20
pool0.240.010.25
qq.chisq000
read.HapMap.data000
read.snps.chiamo000
read.wtccc.signals000
row.summary0.090.000.09
single.snp.tests0.060.020.08
snp-class000
snp.cbind0.220.110.33
snp.clust.plot0.030.000.03
snp.compare0.000.010.08
snp.cor0.910.001.05
snp.dprime-class0.050.020.06
snp.estimates.glm-class000
snp.imputation1.920.112.03
snp.lhs.estimates0.340.050.39
snp.lhs.tests0.100.020.14
snp.matrix-class0.170.000.17
snp.pre.multiply0.090.000.09
snp.reg.imputation-class000
snp.rhs.estimates0.080.000.08
snp.rhs.tests0.050.000.05
snp.tests.glm-class000
snp.tests.single-class000
switch.alleles0.140.030.17
tdt.snp0.010.000.02
test.allele.switch0.140.030.17
testdata0.130.000.12
write.snp.matrix7.280.417.71
xxt0.860.000.86