snpStats 1.1.10
David Clayton
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snpStats | | Last Changed Rev: 53117 / Revision: 53255 | | Last Changed Date: 2011-02-23 09:59:39 -0800 (Wed, 23 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 |
* installing *source* package 'snpStats' ...
Using auto-selected zip option '--use-zip-data'
** libs
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c adler32.c -o adler32.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c bind.c -o bind.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c compress.c -o compress.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c count_gt.c -o count_gt.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c covwin.c -o covwin.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c crc32.c -o crc32.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c deflate.c -o deflate.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c force_hom.c -o force_hom.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c fst.c -o fst.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c glm_test.c -o glm_test.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c gzclose.c -o gzclose.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c gzread.c -o gzread.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c gzwrite.c -o gzwrite.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c hash_index.c -o hash_index.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c hphase.c -o hphase.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c imputation.c -o imputation.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c in.c -o in.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c infback.c -o infback.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c inflate.c -o inflate.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c input.c -o input.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c invert.c -o invert.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c ipf.c -o ipf.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c misc.c -o misc.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c mla.c -o mla.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c outdata.c -o outdata.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c plink.c -o plink.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c read_uncertain.c -o read_uncertain.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c readped.c -o readped.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c single_snp_tests.c -o single_snp_tests.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c snpmpy.c -o snpmpy.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c structure.c -o structure.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c switch.c -o switch.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c tdt.c -o tdt.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c uncertain.c -o uncertain.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -O3 -Wall -std=gnu99 -c uncompr.c -o uncompr.o
gcc -I"E:/biocbld/bbs-2.8-bioc/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 snpStats.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-2.8-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/snpStats.buildbin-libdir/snpStats/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 "snpStats"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snpStats' as snpStats_1.1.10.zip
* DONE (snpStats)