snpMatrix 1.8.0
David Clayton
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/snpMatrix | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/snpMatrix.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snpMatrix/DESCRIPTION' ... OK
* this is package 'snpMatrix' version '1.8.0'
* 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 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 name space can be loaded with stated dependencies ... 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 files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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
* Installing *source* package 'snpMatrix' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c adler32.c -o adler32.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c bind.c -o bind.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c compress.c -o compress.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c covwin.c -o covwin.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c crc32.c -o crc32.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c deflate.c -o deflate.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c force_hom.c -o force_hom.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c glm_test.c -o glm_test.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c glm_test_R.c -o glm_test_R.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c gzio.c -o gzio.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c hash_index.c -o hash_index.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c hphase.c -o hphase.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c ibs.c -o ibs.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c imputation.c -o imputation.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c in.c -o in.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c infback.c -o infback.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c inffast.c -o inffast.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c inflate.c -o inflate.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c inftrees.c -o inftrees.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c input.c -o input.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c invert.c -o invert.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c ld_with.c -o ld_with.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c mla.c -o mla.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c outdata.c -o outdata.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c pairwise_linkage.c -o pairwise_linkage.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c read_chiamo.c -o read_chiamo.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c read_hapmap.c -o read_hapmap.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c read_pedfile.c -o read_pedfile.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c read_signals.c -o read_signals.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c readbed.c -o readbed.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c readped.c -o readped.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c sdfpw.c -o sdfpw.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c single_snp_tests.c -o single_snp_tests.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c snp_summary.c -o snp_summary.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c snpmpy.c -o snpmpy.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c solve_cubic.c -o solve_cubic.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c solve_quadratic.c -o solve_quadratic.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c structure.c -o structure.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c switch.c -o switch.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c tdt.c -o tdt.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c trees.c -o trees.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c uncompr.c -o uncompr.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -O3 -Wall -std=gnu99 -c zutil.c -o zutil.o
gcc -shared -s -o snpMatrix.dll tmp.def adler32.o bind.o compress.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 -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** 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/Updating help pages for package 'snpMatrix'
Formats: text html latex example chm
X.snp-class text html latex example chm
X.snp.matrix-class text html latex example chm
chi.squared text html latex example chm
epsout.ld.snp text html latex example chm
families text html latex example chm
filter.rules text html latex example chm
for.exercise text html latex example chm
glm.test.control text html latex chm
ibs.stats text html latex example chm
ibsCount text html latex example chm
ibsDist text html latex example chm
imputation.maf text html latex example chm
impute.snps text html latex example chm
ld.snp text html latex example chm
ld.with text html latex example chm
misinherits text html latex example chm
pair.result.ld.snp text html latex example chm
plot.snp.dprime text html latex example chm
pool text html latex example chm
pool2 text html latex chm
qq.chisq text html latex example chm
read.HapMap.data text html latex example chm
read.pedfile.info text html latex chm
read.pedfile.map text html latex chm
read.plink text html latex chm
read.snps.chiamo text html latex example chm
read.snps.long text html latex chm
read.snps.pedfile text html latex chm
read.wtccc.signals text html latex example chm
row.summary text html latex example chm
single.snp.tests text html latex example chm
snp-class text html latex example chm
snp.cbind text html latex example chm
snp.cor text html latex example chm
snp.dprime-class text html latex example chm
snp.imputation text html latex example chm
snp.lhs.tests text html latex example chm
snp.matrix-class text html latex example chm
snp.pre text html latex example chm
snp.reg.imputation-class text html latex example chm
snp.rhs.tests text html latex example chm
snp.tests.glm-class text html latex example chm
snp.tests.single-class text html latex example chm
snpMatrix-internal text html latex chm
snpMatrix-package text html latex chm
switch.alleles text html latex example chm
tdt.snp text html latex example chm
test.allele.switch text html latex example chm
testdata text html latex example chm
write.snp.matrix text html latex chm
wtccc.sample.list text html latex chm
xxt text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\SNPMAT~1.RCH\00_PKG~1\SNPMAT~1\chm\snpMatrix.chm
Compile time: 0 minutes, 1 second
53 Topics
397 Local links
26 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\SNPMAT~1.RCH\00_PKG~1\SNPMAT~1\chm\snpMatrix.chm, 119,336 bytes
Compression decreased file by 145,798 bytes.
** building package indices ...
** MD5 sums
* DONE (snpMatrix)