snpMatrix 1.6.1
David Clayton
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/snpMatrix | | Last Changed Rev: 34836 / Revision: 38965 | | Last Changed Date: 2008-10-22 08:29:57 -0700 (Wed, 22 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/snpMatrix.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'snpMatrix/DESCRIPTION' ... OK
* this is package 'snpMatrix' version '1.6.1'
* 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 ... WARNING
Found the following significant warnings:
WARNING: \code inside code block in file 'single.snp.tests.Rd'
WARNING: \code inside code block in file 'single.snp.tests.Rd'
See 'E:/biocbld/bbs-2.3-bioc/meat/snpMatrix.Rcheck/00install.out' for details.
* 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 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
* creating snpMatrix-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating snpMatrix-manual.tex ... OK
* checking snpMatrix-manual.tex using pdflatex ... OK
WARNING: There was 1 warning, see
E:/biocbld/bbs-2.3-bioc/meat/snpMatrix.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/snpMatrix.Rcheck
---------- Making package snpMatrix ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making adler32.d from adler32.c
making bind.d from bind.c
making compress.d from compress.c
making covwin.d from covwin.c
making crc32.d from crc32.c
making deflate.d from deflate.c
making force_hom.d from force_hom.c
making glm_test.d from glm_test.c
making glm_test_R.d from glm_test_R.c
making gzio.d from gzio.c
making hash_index.d from hash_index.c
making ibs.d from ibs.c
making imputation.d from imputation.c
making in.d from in.c
making infback.d from infback.c
making inffast.d from inffast.c
making inflate.d from inflate.c
making inftrees.d from inftrees.c
making input.d from input.c
making inputNew.d from inputNew.c
making input_unsorted.d from input_unsorted.c
making invert.d from invert.c
making ld_graphic_eps.d from ld_graphic_eps.c
making ld_with.d from ld_with.c
making mla.d from mla.c
making outdata.d from outdata.c
making pairwise_linkage.d from pairwise_linkage.c
making read_chiamo.d from read_chiamo.c
making read_hapmap.d from read_hapmap.c
making read_pedfile.d from read_pedfile.c
making read_signals.d from read_signals.c
making readbed.d from readbed.c
making readped.d from readped.c
making sdfpw.d from sdfpw.c
making single_snp_tests.d from single_snp_tests.c
making snp_summary.d from snp_summary.c
making snpmpy.d from snpmpy.c
making solve_cubic.d from solve_cubic.c
making solve_quadratic.d from solve_quadratic.c
making structure.d from structure.c
making switch.d from switch.c
making tdt.d from tdt.c
making trees.d from trees.c
making uncompr.d from uncompr.c
making zutil.d from zutil.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c adler32.c -o adler32.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c bind.c -o bind.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c compress.c -o compress.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c covwin.c -o covwin.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c crc32.c -o crc32.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c deflate.c -o deflate.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c force_hom.c -o force_hom.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_score_test':
glm_test.c:326: warning: unused variable 'test'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:672: warning: unused variable 'err'
glm_test_R.c: In function 'pool2_glm':
glm_test_R.c:867: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:867: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RV' may be used uninitialized in this function
glm_test_R.c:901: warning: 'RU' may be used uninitialized in this function
glm_test_R.c: In function 'snp_lhs_score':
glm_test_R.c:175: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:175: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:285: warning: 'i' may be used uninitialized in this function
glm_test_R.c:205: warning: 'V' may be used uninitialized in this function
glm_test_R.c:205: warning: 'U' may be used uninitialized in this function
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:468: warning: 'Rule_names' may be used uninitialized in this function
glm_test_R.c:592: warning: 'UVnames' may be used uninitialized in this function
glm_test_R.c:592: warning: 'Score' may be used uninitialized in this function
glm_test_R.c:592: warning: 'TestNames' may be used uninitialized in this function
glm_test_R.c:674: warning: 'len' may be used uninitialized in this function
glm_test_R.c:651: warning: 'Snames' may be used uninitialized in this function
glm_test_R.c:651: warning: 'V' may be used uninitialized in this function
glm_test_R.c:651: warning: 'U' may be used uninitialized in this function
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c gzio.c -o gzio.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c hash_index.c -o hash_index.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c ibs.c -o ibs.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c imputation.c -o imputation.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c in.c -o in.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c infback.c -o infback.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c inffast.c -o inffast.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c inflate.c -o inflate.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c inftrees.c -o inftrees.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c input.c -o input.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c inputNew.c -o inputNew.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c input_unsorted.c -o input_unsorted.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c invert.c -o invert.o
invert.c: In function 'syminv':
invert.c:63: warning: unused variable 'nn'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c ld_with.c -o ld_with.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c mla.c -o mla.o
mla.c: In function 'wsum':
mla.c:154: warning: unused variable 'i'
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c outdata.c -o outdata.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c pairwise_linkage.c -o pairwise_linkage.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c read_chiamo.c -o read_chiamo.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c read_hapmap.c -o read_hapmap.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c read_pedfile.c -o read_pedfile.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c read_signals.c -o read_signals.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c readbed.c -o readbed.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c readped.c -o readped.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c sdfpw.c -o sdfpw.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c snp_summary.c -o snp_summary.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c snpmpy.c -o snpmpy.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c solve_cubic.c -o solve_cubic.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c solve_quadratic.c -o solve_quadratic.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c structure.c -o structure.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c switch.c -o switch.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c tdt.c -o tdt.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c trees.c -o trees.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c uncompr.c -o uncompr.o
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c zutil.c -o zutil.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i snpMatrix_res.rc -o snpMatrix_res.o
gcc -std=gnu99 -shared -s -o snpMatrix.dll snpMatrix.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 ibs.o imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.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 snpMatrix_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package snpMatrix for lazy loading
Loading required package: survival
Loading required package: splines
Creating a new generic function for "plot" in "snpMatrix"
installing man source files
installing indices
not zipping data
installing help
>>> 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
Note: removing empty section \references in file 'ibs.stats.Rd'
Note: removing empty section \seealso in file 'ibs.stats.Rd'
Note: removing empty section \references in file 'ibs.stats.Rd'
Note: removing empty section \seealso in file 'ibs.stats.Rd'
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
Note: removing empty section \examples in file 'read.pedfile.info.Rd'
Note: removing empty section \examples in file 'read.pedfile.info.Rd'
read.pedfile.info text html latex chm
Note: removing empty section \examples in file 'read.pedfile.map.Rd'
Note: removing empty section \examples in file 'read.pedfile.map.Rd'
read.pedfile.map text html latex chm
read.plink text html latex chm
Note: removing empty section \note in file 'read.snps.chiamo.Rd'
Note: removing empty section \note in file 'read.snps.chiamo.Rd'
read.snps.chiamo text html latex example chm
read.snps.long text html latex chm
read.snps.long.old text html latex chm
read.snps.pedfile text html latex chm
Note: removing empty section \seealso in file 'read.wtccc.signals.Rd'
Note: removing empty section \seealso in file 'read.wtccc.signals.Rd'
read.wtccc.signals text html latex example chm
row.summary text html latex example chm
WARNING: \code inside code block in file 'single.snp.tests.Rd'
WARNING: \code inside code block in file 'single.snp.tests.Rd'
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
Note: removing empty section \note in file 'wtccc.sample.list.Rd'
Note: removing empty section \examples in file 'wtccc.sample.list.Rd'
Note: removing empty section \note in file 'wtccc.sample.list.Rd'
Note: removing empty section \examples in file 'wtccc.sample.list.Rd'
wtccc.sample.list text html latex chm
xxt text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\snpMatrix.Rcheck\00_pkg_src\snpMatrix\chm\snpMatrix.chm
Compile time: 0 minutes, 1 second
54 Topics
394 Local links
27 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\snpMatrix.Rcheck\00_pkg_src\snpMatrix\chm\snpMatrix.chm, 122,888 bytes
Compression decreased file by 144,782 bytes.
adding MD5 sums
* DONE (snpMatrix)