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This page was generated on 2021-09-20 15:05:30 -0400 (Mon, 20 Sep 2021).

BUILD BIN results for snpStats on tokay2

To the developers/maintainers of the snpStats package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snpStats.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1803/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snpStats 1.42.0  (landing page)
David Clayton
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/snpStats
git_branch: RELEASE_3_13
git_last_commit: 93cc0eb
git_last_commit_date: 2021-05-19 11:40:26 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: snpStats
Version: 1.42.0
Command: rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snpStats.buildbin-libdir snpStats_1.42.0.tar.gz
StartedAt: 2021-09-20 11:28:14 -0400 (Mon, 20 Sep 2021)
EndedAt: 2021-09-20 11:29:52 -0400 (Mon, 20 Sep 2021)
EllapsedTime: 98.1 seconds
RetCode: 0
Status:   OK  
PackageFile: snpStats_1.42.0.zip
PackageFileSize: 7.973 MiB

Command output

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###
### Running command:
###
###   rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snpStats.buildbin-libdir snpStats_1.42.0.tar.gz
###
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install for i386

* installing *source* package 'snpStats' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Runcertain.c -o Runcertain.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bind.c -o bind.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c count_gt.c -o count_gt.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c covwin.c -o covwin.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c force_hom.c -o force_hom.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fst.c -o fst.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c glm_test.c -o glm_test.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hash_index.c -o hash_index.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hphase.c -o hphase.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c imputation.c -o imputation.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c in.c -o in.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input.c -o input.o
input.c: In function 'simplify_names':
input.c:788:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
     strncpy(back, front, MAX_FLD-1);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c: In function 'insnp_new':
input.c:442:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(gtype2, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:438:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(gtype1, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:435:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(cscore, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:432:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(snpid, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:429:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(sampid, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c invert.c -o invert.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ipf.c -o ipf.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ld.c -o ld.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c misc.c -o misc.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mla.c -o mla.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mvphenotype.c -o mvphenotype.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c outdata.c -o outdata.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c plink.c -o plink.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read_uncertain.c -o read_uncertain.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c readped.c -o readped.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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,
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       xadd, xdom);
       ~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c snp_summary.c -o snp_summary.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c snpmpy.c -o snpmpy.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c solve_cubic.c -o solve_cubic.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c structure.c -o structure.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c subset.c -o subset.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tdt.c -o tdt.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c testBig.c -o testBig.o
testBig.c: In function 'snp_big':
testBig.c:31:27: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
     sprintf(name, "Subject%d", i+1);
                           ^~
testBig.c:31:19: note: directive argument in the range [1, 2147483647]
     sprintf(name, "Subject%d", i+1);
                   ^~~~~~~~~~~
testBig.c:31:5: note: 'sprintf' output between 9 and 18 bytes into a destination of size 16
     sprintf(name, "Subject%d", i+1);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c uncertain.c -o uncertain.o
C:/rtools40/mingw32/bin/gcc -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-3.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/snpStats.buildbin-libdir/00LOCK-snpStats/00new/snpStats/libs/i386
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'snpStats' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Runcertain.c -o Runcertain.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bind.c -o bind.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c count_gt.c -o count_gt.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c covwin.c -o covwin.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c force_hom.c -o force_hom.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fst.c -o fst.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c glm_test.c -o glm_test.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hash_index.c -o hash_index.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hphase.c -o hphase.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c imputation.c -o imputation.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c in.c -o in.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input.c -o input.o
input.c: In function 'simplify_names':
input.c:788:5: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
     strncpy(back, front, MAX_FLD-1);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c: In function 'insnp_new':
input.c:442:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(gtype2, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:438:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(gtype1, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:435:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(cscore, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:432:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(snpid, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input.c:429:4: warning: 'strncpy' output may be truncated copying 127 bytes from a string of length 127 [-Wstringop-truncation]
    strncpy(sampid, field, MAX_FLD-1);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c invert.c -o invert.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ipf.c -o ipf.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ld.c -o ld.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c misc.c -o misc.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mla.c -o mla.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mvphenotype.c -o mvphenotype.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c outdata.c -o outdata.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c plink.c -o plink.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read_uncertain.c -o read_uncertain.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c readped.c -o readped.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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,
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       xadd, xdom);
       ~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c snp_summary.c -o snp_summary.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c snpmpy.c -o snpmpy.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c solve_cubic.c -o solve_cubic.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c structure.c -o structure.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c subset.c -o subset.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tdt.c -o tdt.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c testBig.c -o testBig.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c uncertain.c -o uncertain.o
C:/rtools40/mingw64/bin/gcc -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-3.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/snpStats.buildbin-libdir/snpStats/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snpStats' as snpStats_1.42.0.zip
* DONE (snpStats)