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Package 397/436HostnameOS / ArchBUILDCHECKBUILD BIN
snpMatrix2 1.1.8
David Clayton
Snapshot Date: 2011-02-20 11:25:57 -0800 (Sun, 20 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snpMatrix2
Last Changed Rev: 52795 / Revision: 53021
Last Changed Date: 2011-02-16 02:33:51 -0800 (Wed, 16 Feb 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: snpMatrix2
Version: 1.1.8
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings snpMatrix2_1.1.8.tar.gz
StartedAt: 2011-02-20 19:40:51 -0800 (Sun, 20 Feb 2011)
EndedAt: 2011-02-20 19:42:47 -0800 (Sun, 20 Feb 2011)
EllapsedTime: 115.6 seconds
RetCode: 0
Status:  OK  
CheckDir: snpMatrix2.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/snpMatrix2.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 'snpMatrix2/DESCRIPTION' ... OK
* this is package 'snpMatrix2' version '1.1.8'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'snpMatrix2' 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

snpMatrix2.Rcheck/00install.out:

* installing *source* package 'snpMatrix2' ...
** 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 snpMatrix2.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/snpMatrix2.Rcheck/snpMatrix2/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 "snpMatrix2"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (snpMatrix2)

snpMatrix2.Rcheck/snpMatrix2-Ex.timings:

nameusersystemelapsed
Fst0.460.030.48
GlmEstimates-class000
GlmTests-class000
ImputationRules-class000
SingleSnpTests-class000
SnpMatrix-class0.310.070.42
XSnpMatrix-class0.100.000.09
chi.squared0.040.000.10
families0.040.000.03
filter.rules000
for.exercise1.140.001.14
imputation.maf0.000.020.02
impute.snps2.950.093.09
ld0.080.020.13
misinherits0.080.010.09
mvtests000
plotUncertainty000
pool0.290.000.30
qq.chisq000
read.beagle000
read.impute000
read.mach000
row.summary0.140.000.14
single.snp.tests0.100.000.09
snp.cbind0.450.080.53
snp.cor0.940.020.96
snp.imputation3.480.123.64
snp.lhs.estimates0.440.020.45
snp.lhs.tests0.090.000.50
snp.pre.multiply0.220.010.28
snp.rhs.estimates0.10.00.1
snp.rhs.tests0.060.000.06
switch.alleles0.110.000.11
tdt.snp0.030.000.03
test.allele.switch0.20.00.2
testdata0.160.020.17
write.plink0.250.000.25
xxt0.800.010.82