Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:19:07 -0400 (Thu, 12 Apr 2018).
Package 1321/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
snpStats 1.28.0 David Clayton
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: snpStats |
Version: 1.28.0 |
Command: rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/snpStats_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=snpStats.buildbin-libdir --merge-multiarch snpStats_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL snpStats_1.28.0.zip && rm snpStats_1.28.0.tar.gz snpStats_1.28.0.zip |
StartedAt: 2018-04-11 18:28:13 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 18:31:22 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 189.1 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/snpStats_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=snpStats.buildbin-libdir --merge-multiarch snpStats_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL snpStats_1.28.0.zip && rm snpStats_1.28.0.tar.gz snpStats_1.28.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 4599k 100 4599k 0 0 72.0M 0 --:--:-- --:--:-- --:--:-- 76.1M install for i386 * installing *source* package 'snpStats' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c Runcertain.c -o Runcertain.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c bind.c -o bind.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c count_gt.c -o count_gt.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c covwin.c -o covwin.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c force_hom.c -o force_hom.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c fst.c -o fst.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c glm_test.c -o glm_test.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c glm_test_R.c -o glm_test_R.o glm_test_R.c: In function 'snp_rhs_score': glm_test_R.c:368:7: warning: unused variable 'max_name_length' [-Wunused-variable] int max_name_length = MAX_NAME_LENGTH -1; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c hash_index.c -o hash_index.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c hphase.c -o hphase.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c imputation.c -o imputation.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c in.c -o in.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c input.c -o input.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c invert.c -o invert.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c ipf.c -o ipf.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c ld.c -o ld.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c misc.c -o misc.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c mla.c -o mla.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c mvphenotype.c -o mvphenotype.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c outdata.c -o outdata.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c plink.c -o plink.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_uncertain.c -o read_uncertain.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c readped.c -o readped.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c single_snp_tests.c -o single_snp_tests.o single_snp_tests.c: In function 'score_single': single_snp_tests.c:327:4: warning: 'name_index' may be used uninitialized in this function [-Wmaybe-uninitialized] do_impute(Snps, n, diploid, subset, nsubj, name_index, Rule, gt2ht, ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c snp_summary.c -o snp_summary.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c snpmpy.c -o snpmpy.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c solve_cubic.c -o solve_cubic.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c structure.c -o structure.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c subset.c -o subset.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c switch.c -o switch.o switch.c: In function 'test_switch': switch.c:32:8: warning: variable 'female2' set but not used [-Wunused-but-set-variable] int *female2 = NULL; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c tdt.c -o tdt.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c testBig.c -o testBig.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c uncertain.c -o uncertain.o C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o snpStats.dll tmp.def Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.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 subset.o switch.o tdt.o testBig.o uncertain.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/i386 ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'snpStats' finding HTML links ... done Fst html GlmEstimates-class html GlmTests-class html ImputationRules-class html SingleSnpTests-class html SnpMatrix-class html XSnpMatrix-class html chi.squared html convert.snpMatrix html example-new html families html filter.rules html for.exercise html glm.test.control html ibsCount html ibsDist html imputation.maf html impute.snps html ld html ld.example html mean2g html misinherits html mvtests html plotUncertainty html pool html pool2 html pp html qq.chisq html random.snps html read.beagle html read.impute html read.long html read.mach html read.pedfile html read.plink html read.snps.long html row.summary html sample html single.snp.tests html sm.compare html snp.cor html snp.imputation html snp.lhs.estimates html snp.lhs.tests html snp.pre.multiply html snp.rhs.estimates html snp.rhs.tests html snpStats-package html switch.alleles html tdt.snp html test.allele.switch html testdata html write.plink html write.snp.matrix html xxt html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'snpStats' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c Runcertain.c -o Runcertain.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c bind.c -o bind.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c count_gt.c -o count_gt.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c covwin.c -o covwin.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c force_hom.c -o force_hom.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c fst.c -o fst.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c glm_test.c -o glm_test.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c glm_test_R.c -o glm_test_R.o glm_test_R.c: In function 'snp_rhs_score': glm_test_R.c:368:7: warning: unused variable 'max_name_length' [-Wunused-variable] int max_name_length = MAX_NAME_LENGTH -1; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c hash_index.c -o hash_index.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c hphase.c -o hphase.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c imputation.c -o imputation.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c in.c -o in.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c input.c -o input.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c invert.c -o invert.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c ipf.c -o ipf.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c ld.c -o ld.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c misc.c -o misc.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c mla.c -o mla.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c mvphenotype.c -o mvphenotype.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c outdata.c -o outdata.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c plink.c -o plink.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_uncertain.c -o read_uncertain.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c readped.c -o readped.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c single_snp_tests.c -o single_snp_tests.o single_snp_tests.c: In function 'score_single': single_snp_tests.c:327:4: warning: 'name_index' may be used uninitialized in this function [-Wmaybe-uninitialized] do_impute(Snps, n, diploid, subset, nsubj, name_index, Rule, gt2ht, ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c snp_summary.c -o snp_summary.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c snpmpy.c -o snpmpy.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c solve_cubic.c -o solve_cubic.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c structure.c -o structure.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c subset.c -o subset.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c switch.c -o switch.o switch.c: In function 'test_switch': switch.c:32:8: warning: variable 'female2' set but not used [-Wunused-but-set-variable] int *female2 = NULL; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c tdt.c -o tdt.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c testBig.c -o testBig.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c uncertain.c -o uncertain.o C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o snpStats.dll tmp.def Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.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 subset.o switch.o tdt.o testBig.o uncertain.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'snpStats' as snpStats_1.28.0.zip * DONE (snpStats) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library' package 'snpStats' successfully unpacked and MD5 sums checked In R CMD INSTALL