Package: groHMM

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:groHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings groHMM_1.16.0.tar.gz

StartedAt: 2019-04-13 02:53:43 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:58:28 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 285.4 seconds

RetCode: 0

Status:  OK

CheckDir: groHMM.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:groHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings groHMM_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/groHMM.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'groHMM/DESCRIPTION' ... OK
* this is package 'groHMM' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Depends: includes the non-default packages:
  'MASS' 'parallel' 'S4Vectors' 'IRanges' 'GenomeInfoDb'
  'GenomicRanges' 'GenomicAlignments' 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'groHMM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/groHMM/libs/i386/groHMM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/groHMM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/groHMM_1.16.0.tar.gz && rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=groHMM.buildbin-libdir groHMM_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL groHMM_1.16.0.zip && rm groHMM_1.16.0.tar.gz groHMM_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3954k  100 3954k    0     0  38.2M      0 --:--:-- --:--:-- --:--:-- 39.8M

install for i386

* installing *source* package 'groHMM' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c AnnotateProbes.c -o AnnotateProbes.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c DecayAlgorithm.c -o DecayAlgorithm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c RegisterRRoutines.c -o RegisterRRoutines.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c hmmEM.c -o hmmEM.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmEM.c:51:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmFwBw.c:46:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:36:0,
                 from hmmMiscFunctions.c:44:
hmmMiscFunctions.c: 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:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmViterbi.c:49:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_32/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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/groHMM.buildbin-libdir/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
In R CMD INSTALL

install for x64

* installing *source* package 'groHMM' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c AnnotateProbes.c -o AnnotateProbes.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c DecayAlgorithm.c -o DecayAlgorithm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c RegisterRRoutines.c -o RegisterRRoutines.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c hmmEM.c -o hmmEM.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmEM.c:51:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmFwBw.c:46:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:36:0,
                 from hmmMiscFunctions.c:44:
hmmMiscFunctions.c: 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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmHeader.h:36:0,
                 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;
               ^
In file included from hmmViterbi.c:49:0:
hmmHeader.h:281:16: warning: 'MargainalizeSumLogProbOver' defined but not used [-Wunused-function]
 static  double MargainalizeSumLogProbOver(int state, int position, 
                ^
hmmHeader.h:301:16: warning: 'expSum' defined but not used [-Wunused-function]
 static  double expSum(double *logValues, int length) {
                ^
C:/Rtools/mingw_64/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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'groHMM' as groHMM_1.16.0.zip
* DONE (groHMM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'groHMM' successfully unpacked and MD5 sums checked
In R CMD INSTALL