snpStats 1.4.1
David Clayton
| Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/snpStats | | Last Changed Rev: 61454 / Revision: 64395 | | Last Changed Date: 2011-12-19 07:48:37 -0800 (Mon, 19 Dec 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/snpStats.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snpStats/DESCRIPTION' ... OK
* this is package 'snpStats' version '1.4.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'snpStats' can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.0Mb
sub-directories of 1Mb or more:
data 6.4Mb
doc 2.3Mb
* 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
* loading checks for arch 'i386'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
families.RData 46Kb 26Kb xz
for.exercise.RData 5.4Mb 3.5Mb xz
ld.example.RData 28Kb 20Kb xz
testdata.RData 875Kb 557Kb xz
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'D:/biocbld/bbs-2.9-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/i386/snpStats.dll':
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
install for i386
* installing *source* package 'snpStats' ...
** libs
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c adler32.c -o adler32.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bind.c -o bind.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c compress.c -o compress.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c count_gt.c -o count_gt.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c covwin.c -o covwin.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c crc32.c -o crc32.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c deflate.c -o deflate.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c force_hom.c -o force_hom.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fst.c -o fst.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_fit':
glm_test.c:255:26: warning: 'dfr' may be used uninitialized in this function [-Wuninitialized]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:364:8: warning: variable 'testname' set but not used [-Wunused-but-set-variable]
glm_test_R.c: In function 'snp_rhs_estimate':
glm_test_R.c:1501:11: warning: variable 'Uc' set but not used [-Wunused-but-set-variable]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c gzclose.c -o gzclose.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c gzread.c -o gzread.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c gzwrite.c -o gzwrite.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hash_index.c -o hash_index.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hphase.c -o hphase.o
hphase.c: In function 'emhap':
hphase.c:261:9: warning: variable 'ipfault' set but not used [-Wunused-but-set-variable]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c imputation.c -o imputation.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c in.c -o in.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c infback.c -o infback.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c inflate.c -o inflate.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c input.c -o input.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c invert.c -o invert.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ipf.c -o ipf.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ld.c -o ld.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c misc.c -o misc.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mla.c -o mla.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mvphenotype.c -o mvphenotype.o
mvphenotype.c: In function 'mvphen':
mvphenotype.c:190:7: warning: variable 'ifX' set but not used [-Wunused-but-set-variable]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c outdata.c -o outdata.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c plink.c -o plink.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c read_uncertain.c -o read_uncertain.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c readped.c -o readped.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c single_snp_tests.c -o single_snp_tests.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c snp_summary.c -o snp_summary.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c snpmpy.c -o snpmpy.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c solve_cubic.c -o solve_cubic.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c structure.c -o structure.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c switch.c -o switch.o
switch.c: In function 'test_switch':
switch.c:52:10: warning: variable 'fg' set but not used [-Wunused-but-set-variable]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c tdt.c -o tdt.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
trees.c: In function '_tr_stored_block':
trees.c:883:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_align':
trees.c:919:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_flush_block':
trees.c:1020:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_tally':
trees.c:1071:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: At top level:
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c uncertain.c -o uncertain.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c uncompr.c -o uncompr.o
gcc -I"D:/biocbld/BBS-2˜1.9-B/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c zutil.c -o zutil.o
zutil.c: In function 'zcalloc':
zutil.c:308:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
zutil.c: In function 'zcfree':
zutil.c:316:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
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 -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'snpStats'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'data-input-vignette.Rnw'
'differences.Rnw'
'imputation-vignette.Rnw'
'ld-vignette.Rnw'
'pca-vignette.Rnw'
'snpStats-vignette.Rnw'
'tdt-vignette.Rnw'
** testing if installed package can be loaded
add DLL for x64
* installing *source* package 'snpStats' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c adler32.c -o adler32.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bind.c -o bind.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c compress.c -o compress.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c count_gt.c -o count_gt.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c covwin.c -o covwin.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c crc32.c -o crc32.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c deflate.c -o deflate.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c force_hom.c -o force_hom.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c fst.c -o fst.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c glm_test.c -o glm_test.o
glm_test.c: In function 'glm_fit':
glm_test.c:255:26: warning: 'dfr' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c glm_test_R.c -o glm_test_R.o
glm_test_R.c: In function 'snp_rhs_score':
glm_test_R.c:364:8: warning: variable 'testname' set but not used [-Wunused-but-set-variable]
glm_test_R.c: In function 'snp_rhs_estimate':
glm_test_R.c:1501:11: warning: variable 'Uc' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c gzclose.c -o gzclose.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c gzread.c -o gzread.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c gzwrite.c -o gzwrite.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hash_index.c -o hash_index.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hphase.c -o hphase.o
hphase.c: In function 'emhap':
hphase.c:261:9: warning: variable 'ipfault' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c imputation.c -o imputation.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c in.c -o in.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c infback.c -o infback.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c inflate.c -o inflate.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c input.c -o input.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c invert.c -o invert.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ipf.c -o ipf.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ld.c -o ld.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c misc.c -o misc.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mla.c -o mla.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mvphenotype.c -o mvphenotype.o
mvphenotype.c: In function 'mvphen':
mvphenotype.c:190:7: warning: variable 'ifX' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c outdata.c -o outdata.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c plink.c -o plink.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c read_uncertain.c -o read_uncertain.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c readped.c -o readped.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c single_snp_tests.c -o single_snp_tests.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c snp_summary.c -o snp_summary.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c snpmpy.c -o snpmpy.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c solve_cubic.c -o solve_cubic.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c structure.c -o structure.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c switch.c -o switch.o
switch.c: In function 'test_switch':
switch.c:52:10: warning: variable 'fg' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c tdt.c -o tdt.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -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 [-Wattributes]
trees.c: In function '_tr_stored_block':
trees.c:883:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_align':
trees.c:919:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_flush_block':
trees.c:1020:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: In function '_tr_tally':
trees.c:1071:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c: At top level:
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
trees.c:1244:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c uncertain.c -o uncertain.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c uncompr.c -o uncompr.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c zutil.c -o zutil.o
zutil.c: In function 'zcalloc':
zutil.c:308:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
zutil.c: In function 'zcfree':
zutil.c:316:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
gcc -m64 -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 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snpStats' as snpStats_1.4.1.zip
* DONE (snpStats)