Package: snpAssoc

Version: 1.1.9

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings snpAssoc_1.1.9.tar.gz

StartedAt: 2011-02-22 20:02:12 -0800 (Tue, 22 Feb 2011)

EndedAt: 2011-02-22 20:04:09 -0800 (Tue, 22 Feb 2011)

EllapsedTime: 117.0 seconds

RetCode: 0

Status:  OK

CheckDir: snpAssoc.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/snpAssoc.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snpAssoc/DESCRIPTION' ... OK
* this is package 'snpAssoc' version '1.1.9'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'snpAssoc' 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 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 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 'snpAssoc' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c adler32.c -o adler32.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c bind.c -o bind.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c compress.c -o compress.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c count_gt.c -o count_gt.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c covwin.c -o covwin.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c crc32.c -o crc32.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c deflate.c -o deflate.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c force_hom.c -o force_hom.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c fst.c -o fst.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c glm_test.c -o glm_test.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:688:11: warning: unused variable 'len'
glm_test_R.c: In function 'pool2_glm':
glm_test_R.c:939:12: warning: unused variable 'Unames'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c gzclose.c -o gzclose.o
gcc -I"E:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c gzread.c -o gzread.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c gzwrite.c -o gzwrite.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c hash_index.c -o hash_index.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c hphase.c -o hphase.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c imputation.c -o imputation.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c in.c -o in.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c infback.c -o infback.o
gcc -I"E:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c inflate.c -o inflate.o
gcc -I"E:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c input.c -o input.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c invert.c -o invert.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c ipf.c -o ipf.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c ld.c -o ld.o
ld.c: In function 'ld':
ld.c:168:12: warning: unused variable 'ld'
ld.c:184:12: warning: unused variable 'ld'
ld.c: In function 'phase':
ld.c:263:10: warning: 'llh' may be used uninitialized in this function
ld.c: In function 'ld':
ld.c:59:18: warning: 'y' may be used uninitialized in this function
ld.c:81:8: warning: 'Result' may be used uninitialized in this function
ld.c:81:16: warning: 'Snames' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c misc.c -o misc.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c mla.c -o mla.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c mvphenotype.c -o mvphenotype.o
mvphenotype.c: In function 'mvphen':
mvphenotype.c:544:15: warning: unused variable 'Udnames'
mvphenotype.c:405:10: warning: unused variable 'testname'
mvphenotype.c:404:9: warning: unused variable 'space'
mvphenotype.c:296:16: warning: unused variable 'TestNames'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c outdata.c -o outdata.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c plink.c -o plink.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c read_uncertain.c -o read_uncertain.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c readped.c -o readped.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c single_snp_tests.c -o single_snp_tests.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c snp_summary.c -o snp_summary.o
snp_summary.c: In function 'X_snp_summary':
snp_summary.c:127:11: warning: 'add' may be used uninitialized in this function
snp_summary.c:127:17: warning: 'dom' may be used uninitialized in this function
snp_summary.c:128:7: warning: 'pmax' may be used uninitialized in this function
snp_summary.c: In function 'snp_summary':
snp_summary.c:384:11: warning: 'add' may be used uninitialized in this function
snp_summary.c:384:17: warning: 'dom' may be used uninitialized in this function
snp_summary.c:385:7: warning: 'pmax' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c snpmpy.c -o snpmpy.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c solve_cubic.c -o solve_cubic.o
solve_cubic.c:29:0: warning: "M_PI" redefined
c:\rtools212\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/math.h:58:0: note: this is the location of the previous definition
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c structure.c -o structure.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c switch.c -o switch.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c tdt.c -o tdt.o
gcc -I"E:/biocbld/BBS-2˜1.8-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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c uncertain.c -o uncertain.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c uncompr.c -o uncompr.o
gcc -I"E:/biocbld/BBS-2˜1.8-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 snpAssoc.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 imputation.o in.o infback.o inffast.o inflate.o inftrees.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o switch.o tdt.o trees.o uncertain.o uncompr.o zutil.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/snpAssoc.Rcheck/snpAssoc/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: splines
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Creating a new generic function for "plot" in "snpAssoc"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (snpAssoc)

name	user	system	elapsed
Fst	0.47	0.00	0.56
GlmEstimates-class	0	0	0
GlmTests-class	0	0	0
ImputationRules-class	0	0	0
SingleSnpTests-class	0	0	0
SnpMatrix-class	1.06	0.07	1.13
XSnpMatrix-class	0.22	0.00	0.22
chi.squared	0.08	0.00	0.09
families	0.03	0.00	0.03
filter.rules	0	0	0
for.exercise	1.08	0.03	1.11
imputation.maf	0	0	0
impute.snps	4.95	0.11	5.09
ld	0.11	0.00	0.13
misinherits	0.08	0.01	0.09
mvtests	0	0	0
plotUncertainty	0	0	0
pool	0.22	0.00	0.22
qq.chisq	0	0	0
read.beagle	0	0	0
read.impute	0	0	0
read.mach	0	0	0
row.summary	0.12	0.02	0.14
single.snp.tests	0.08	0.00	0.08
snp.cbind	0.49	0.03	0.53
snp.cor	0.92	0.01	0.94
snp.imputation	3.59	0.16	3.75
snp.lhs.estimates	0.38	0.00	0.37
snp.lhs.tests	0.11	0.02	0.13
snp.pre.multiply	0.09	0.01	0.11
snp.rhs.estimates	0.08	0.00	0.07
snp.rhs.tests	0.06	0.00	0.07
switch.alleles	0.22	0.00	0.22
tdt.snp	0.03	0.00	0.03
test.allele.switch	0.15	0.00	0.16
testdata	0.16	0.00	0.16
write.plink	0.22	0.03	0.25
xxt	0.80	0.00	0.79