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This page was generated on 2022-06-27 11:09:56 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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CHECK results for groHMM on nebbiolo1


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 850/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.30.1  (landing page)
Anusha Nagari , Tulip Nandu , W. Lee Kraus
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/groHMM
git_branch: RELEASE_3_15
git_last_commit: efe650e
git_last_commit_date: 2022-05-11 18:52:12 -0400 (Wed, 11 May 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: groHMM
Version: 1.30.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings groHMM_1.30.1.tar.gz
StartedAt: 2022-06-26 20:09:31 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:12:46 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 195.5 seconds
RetCode: 0
Status:   OK  
CheckDir: groHMM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:groHMM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings groHMM_1.30.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/groHMM.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘groHMM/DESCRIPTION’ ... OK
* this is package ‘groHMM’ version ‘1.30.1’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/groHMM.Rcheck/00check.log’
for details.



Installation output

groHMM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL groHMM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:43:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Windowing.c -o Windowing.o
Windowing.c: In function ‘WindowAnalysis’:
Windowing.c:146:6: warning: unused variable ‘II’ [-Wunused-variable]
  146 |  int II = 0;
      |      ^~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmEM.c:50:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function ‘forward’:
hmmFwBw.c:142:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  142 |       for(k=1; k<n; k++)
      |       ^~~
hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  145 |         for (k = 0; k<n; k++) {
      |         ^~~
In file included from hmmFwBw.c:45:
At top level:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmFwBw.c:45:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function ‘SStatsNormExp’:
hmmMiscFunctions.c:384:10: warning: unused variable ‘wi’ [-Wunused-variable]
  384 |   double wi, *newEx;
      |          ^~
hmmMiscFunctions.c: In function ‘UpdateNormExp’:
hmmMiscFunctions.c:417:10: warning: unused variable ‘epsilon’ [-Wunused-variable]
  417 |   double epsilon=0.00001;
      |          ^~~~~~~
In file included from hmmHeader.h:36,
                 from hmmMiscFunctions.c:43:
At top level:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:48:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
  301 | static  double expSum(double *logValues, int length) {
      |                ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
  281 | static  double MargainalizeSumLogProbOver(int state, int position,
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36,
                 from hmmViterbi.c:48:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
   39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
      |               ^~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-groHMM/00new/groHMM/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (groHMM)

Tests output


Example timings

groHMM.Rcheck/groHMM-Ex.timings

nameusersystemelapsed
breakTranscriptsOnGenes0.8160.1400.956
combineTranscripts0.4830.1000.583
detectTranscripts0.6440.2201.460
evaluateHMMInAnnotations0.2250.0670.488
getCores000
getTxDensity0.0370.0040.089
limitToXkb0.1600.0030.263
makeConsensusAnnotations0.0010.0000.001
metaGene0.2710.0120.292
pausingIndex1.3710.4441.815
polymeraseWave0.8380.1120.963
runMetaGene0.0370.0000.038
windowAnalysis0.3840.0080.393
writeWiggle0.3890.0400.429