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BUILD BIN report for groHMM on tokay2

This page was generated on 2020-10-17 11:56:46 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE groHMM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 779/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.22.0
Anusha Nagari , Tulip Nandu , W. Lee Kraus
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/groHMM
Branch: RELEASE_3_11
Last Commit: 65b3070
Last Changed Date: 2020-04-27 14:44:49 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: groHMM
Version: 1.22.0
Command: rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=groHMM.buildbin-libdir groHMM_1.22.0.tar.gz
StartedAt: 2020-10-17 10:42:36 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 10:43:56 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 79.8 seconds
RetCode: 0
Status:  OK  
PackageFile: groHMM_1.22.0.zip
PackageFileSize: 4.307 MiB

Command output

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### Running command:
###
###   rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=groHMM.buildbin-libdir groHMM_1.22.0.tar.gz
###
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install for i386

* installing *source* package 'groHMM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AnnotateProbes.c -o AnnotateProbes.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DecayAlgorithm.c -o DecayAlgorithm.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RegisterRRoutines.c -o RegisterRRoutines.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
  int II = 0;
      ^~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:51:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmEM.c:51:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function 'forward':
hmmFwBw.c:143:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
       for(k=1; k<n; k++)
       ^~~
hmmFwBw.c:146:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
         for (k = 0; k<n; k++) {
         ^~~
In file included from hmmFwBw.c:46:
At top level:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmFwBw.c:46:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
   double wi, *newEx;
          ^~
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
   double epsilon=0.00001;
          ^~~~~~~
In file included from hmmHeader.h:36,
                 from hmmMiscFunctions.c:44:
At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:49:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmViterbi.c:49:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/groHMM.buildbin-libdir/00LOCK-groHMM/00new/groHMM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'groHMM'
    finding HTML links ... done
    RgammaMLE                               html  
    Rnorm                                   html  
    Rnorm.exp                               html  
    averagePlot                             html  
    breakTranscriptsOnGenes                 html  
    combineTranscripts                      html  
    countMappableReadsInInterval            html  
    detectTranscripts                       html  
    evaluateHMMInAnnotations                html  
    expressedGenes                          html  
    getCores                                html  
    getTxDensity                            html  
    groHMM-package                          html  
    limitToXkb                              html  
    makeConsensusAnnotations                html  
    metaGene                                html  
    metaGeneMatrix                          html  
    metaGene_nL                             html  
    pausingIndex                            html  
    polymeraseWave                          html  
    readBed                                 html  
    runMetaGene                             html  
    tlsDeming                               html  
    tlsLoess                                html  
    tlsSvd                                  html  
    windowAnalysis                          html  
    writeWiggle                             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 'groHMM' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c AnnotateProbes.c -o AnnotateProbes.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c DecayAlgorithm.c -o DecayAlgorithm.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RegisterRRoutines.c -o RegisterRRoutines.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Windowing.c -o Windowing.o
Windowing.c: In function 'WindowAnalysis':
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
  int II = 0;
      ^~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:51:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmEM.c:51:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function 'forward':
hmmFwBw.c:143:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
       for(k=1; k<n; k++)
       ^~~
hmmFwBw.c:146:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
         for (k = 0; k<n; k++) {
         ^~~
In file included from hmmFwBw.c:46:
At top level:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmFwBw.c:46:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function 'SStatsNormExp':
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
   double wi, *newEx;
          ^~
hmmMiscFunctions.c: In function 'UpdateNormExp':
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
   double epsilon=0.00001;
          ^~~~~~~
In file included from hmmHeader.h:36,
                 from hmmMiscFunctions.c:44:
At top level:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:49:
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^~~~~~
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position,
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmViterbi.c:49:
UsefulValues.h:39:15: warning: 'VERY_LARGE_DOUBLE_VALUE' defined but not used [-Wunused-variable]
 static double VERY_LARGE_DOUBLE_VALUE = 1e20;
               ^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o groHMM.dll tmp.def AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'groHMM' as groHMM_1.22.0.zip
* DONE (groHMM)