Back to Multiple platform build/check report for BioC 3.14
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:40 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for groHMM on tokay2


To the developers/maintainers of the groHMM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/groHMM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 826/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.28.0  (landing page)
Anusha Nagari , Tulip Nandu , W. Lee Kraus
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/groHMM
git_branch: RELEASE_3_14
git_last_commit: 6432fd9
git_last_commit_date: 2021-10-26 12:17:11 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    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: groHMM
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:groHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings groHMM_1.28.0.tar.gz
StartedAt: 2022-04-12 20:49:26 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 20:53:39 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 253.4 seconds
RetCode: 0
Status:   OK  
CheckDir: groHMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:groHMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings groHMM_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/groHMM.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... 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-3.14-bioc/R/library/groHMM/libs/i386/groHMM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/groHMM/libs/x64/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-3.14-bioc/meat/groHMM.Rcheck/00check.log'
for details.



Installation output

groHMM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/groHMM_1.28.0.tar.gz && rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=groHMM.buildbin-libdir groHMM_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL groHMM_1.28.0.zip && rm groHMM_1.28.0.tar.gz groHMM_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
  8 3955k    8  347k    0     0   584k      0  0:00:06 --:--:--  0:00:06  583k
 43 3955k   43 1709k    0     0  1072k      0  0:00:03  0:00:01  0:00:02 1071k
100 3955k  100 3955k    0     0  1544k      0  0:00:02  0:00:02 --:--:-- 1545k

install for i386

* installing *source* package 'groHMM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/groHMM.buildbin-libdir/groHMM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'groHMM' as groHMM_1.28.0.zip
* DONE (groHMM)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'groHMM' successfully unpacked and MD5 sums checked

Tests output


Example timings

groHMM.Rcheck/examples_i386/groHMM-Ex.timings

nameusersystemelapsed
breakTranscriptsOnGenes0.500.170.68
combineTranscripts0.280.150.43
detectTranscripts0.460.050.64
evaluateHMMInAnnotations0.150.000.16
getCores000
getTxDensity0.040.000.03
limitToXkb0.100.000.11
makeConsensusAnnotations000
metaGene0.110.000.11
pausingIndex0.290.010.29
polymeraseWave1.430.051.58
runMetaGene0.030.000.03
windowAnalysis0.220.020.24
writeWiggle0.240.010.25

groHMM.Rcheck/examples_x64/groHMM-Ex.timings

nameusersystemelapsed
breakTranscriptsOnGenes0.550.010.57
combineTranscripts0.330.080.40
detectTranscripts0.450.020.47
evaluateHMMInAnnotations0.160.000.15
getCores000
getTxDensity0.030.000.03
limitToXkb0.720.000.72
makeConsensusAnnotations000
metaGene0.090.000.09
pausingIndex0.270.000.27
polymeraseWave0.600.110.72
runMetaGene0.040.000.03
windowAnalysis0.200.030.23
writeWiggle0.190.060.25