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This page was generated on 2022-10-19 13:22:19 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for snpStats on palomino3


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? for more information.
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raw results

Package 1880/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snpStats 1.46.0  (landing page)
David Clayton
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/snpStats
git_branch: RELEASE_3_15
git_last_commit: 1e70784
git_last_commit_date: 2022-04-26 11:00:54 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: snpStats
Version: 1.46.0
Command: rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=snpStats.buildbin-libdir snpStats_1.46.0.tar.gz
StartedAt: 2022-10-19 06:37:02 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 06:38:00 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 58.3 seconds
RetCode: 0
Status:   OK  
PackageFile: snpStats_1.46.0.zip
PackageFileSize: 7.536 MiB

Command output

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###
### Running command:
###
###   rm -rf snpStats.buildbin-libdir && mkdir snpStats.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=snpStats.buildbin-libdir snpStats_1.46.0.tar.gz
###
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* installing *source* package 'snpStats' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Runcertain.c -o Runcertain.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bind.c -o bind.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c count_gt.c -o count_gt.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c covwin.c -o covwin.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c force_hom.c -o force_hom.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fst.c -o fst.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c glm_test.c -o glm_test.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  368 |   int max_name_length =  MAX_NAME_LENGTH -1;
      |       ^~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hash_index.c -o hash_index.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hphase.c -o hphase.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c imputation.c -o imputation.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c in.c -o in.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  788 |     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]
  442 |    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]
  438 |    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]
  435 |    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]
  432 |    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]
  429 |    strncpy(sampid, field, MAX_FLD-1);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c invert.c -o invert.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ipf.c -o ipf.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ld.c -o ld.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c misc.c -o misc.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mla.c -o mla.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mvphenotype.c -o mvphenotype.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c outdata.c -o outdata.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c plink.c -o plink.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read_uncertain.c -o read_uncertain.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c readped.c -o readped.o
readped.c: In function 'readped':
readped.c:234:33: warning: '%d' directive output may be truncated writing between 1 and 11 bytes into a region of size between 0 and 127 [-Wformat-truncation=]
  234 |     snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
      |                                 ^~
readped.c:234:5: note: 'snprintf' output between 3 and 140 bytes into a destination of size 128
  234 |     snprintf(fmid, MAX_ID, "%s%c%d", fid, sepchar, memi);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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:223:4: warning: 'name_index' may be used uninitialized in this function [-Wmaybe-uninitialized]
  223 |    do_impute(Snps, n, NULL, subset, nsubj, name_index, Rule, gt2ht,
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  224 |       xadd, xdom);
      |       ~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c snp_summary.c -o snp_summary.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c snpmpy.c -o snpmpy.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c solve_cubic.c -o solve_cubic.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c structure.c -o structure.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c subset.c -o subset.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
   32 |   int *female2 = NULL;
      |        ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tdt.c -o tdt.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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=]
   31 |     sprintf(name, "Subject%d", i+1);
      |                           ^~
testBig.c:31:19: note: directive argument in the range [1, 2147483647]
   31 |     sprintf(name, "Subject%d", i+1);
      |                   ^~~~~~~~~~~
testBig.c:31:5: note: 'sprintf' output between 9 and 18 bytes into a destination of size 16
   31 |     sprintf(name, "Subject%d", i+1);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c uncertain.c -o uncertain.o
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 -LF:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/meat/snpStats.buildbin-libdir/00LOCK-snpStats/00new/snpStats/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'snpStats' as snpStats_1.46.0.zip
* DONE (snpStats)