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BioC 3.6: CHECK report for groHMM on veracruz1

This page was generated on 2017-08-16 13:46:13 -0400 (Wed, 16 Aug 2017).

Package 603/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.11.0
Anusha Nagari , Venkat Malladi , Tulip Nandu , W. Lee Kraus
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/groHMM
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: groHMM
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings groHMM_1.11.0.tar.gz
StartedAt: 2017-08-16 04:05:10 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:08:32 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 202.1 seconds
RetCode: 0
Status:  OK 
CheckDir: groHMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings groHMM_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/groHMM.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘groHMM/DESCRIPTION’ ... OK
* this is package ‘groHMM’ version ‘1.11.0’
* 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 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 ... NOTE
Authors@R field gives more than one person with maintainer role:
  Minho Chae <minho.chae@gmail.com> [aut, cre]
  W. Lee Kraus <lee.kraus@utsouthwestern.edu> [aut, cre]
* 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 loading without being on the library search path ... 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 ... NOTE
approx.ratio.CI: no visible global function definition for ‘qnorm’
breakTranscriptsOnGenes: no visible global function definition for
  ‘par’
combineTranscripts: no visible global function definition for ‘par’
expressedGenes_foreachChrom: no visible global function definition for
  ‘ppois’
getTxDensity: no visible global function definition for ‘abline’
pausingIndex_foreachChrom : <anonymous>: no visible global function
  definition for ‘fisher.test’
plot2Ranges: no visible global function definition for ‘plot.new’
plot2Ranges: no visible global function definition for ‘plot.window’
plot2Ranges: no visible global function definition for ‘rect’
plot2Ranges: no visible global function definition for ‘rgb’
plot2Ranges: no visible global function definition for ‘text’
plot2Ranges: no visible global function definition for ‘title’
plot2Ranges: no visible global function definition for ‘axis’
polymeraseWave: no visible global function definition for ‘smooth’
polymeraseWave: no visible global function definition for ‘hist’
polymeraseWave: no visible global function definition for ‘ks.test’
polymeraseWave: no visible global function definition for ‘dnorm’
polymeraseWave: no visible global function definition for ‘dexp’
polymeraseWave: no visible global function definition for ‘dgamma’
readBed: no visible global function definition for ‘read.table’
tlsLoess: no visible global function definition for ‘loess’
tlsLoess: no visible global function definition for ‘predict’
Undefined global functions or variables:
  abline axis dexp dgamma dnorm fisher.test hist ks.test loess par
  plot.new plot.window ppois predict qnorm read.table rect rgb smooth
  text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "hist", "par", "plot.new",
             "plot.window", "rect", "text", "title")
  importFrom("stats", "dexp", "dgamma", "dnorm", "fisher.test",
             "ks.test", "loess", "ppois", "predict", "qnorm", "smooth")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/groHMM.Rcheck/00check.log’
for details.


groHMM.Rcheck/00install.out:

* installing *source* package ‘groHMM’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c AnnotateProbes.c -o AnnotateProbes.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DecayAlgorithm.c -o DecayAlgorithm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c RegisterRRoutines.c -o RegisterRRoutines.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Windowing.c -o Windowing.o
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
        int II = 0;
            ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:51:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmFwBw.c:46:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
  double wi, *newEx;
         ^
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
  double epsilon=0.00001;
         ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:49:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/groHMM.Rcheck/groHMM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (groHMM)

groHMM.Rcheck/groHMM-Ex.timings:

nameusersystemelapsed
breakTranscriptsOnGenes1.3930.0171.445
combineTranscripts0.5140.0020.527
detectTranscripts0.7700.0150.804
evaluateHMMInAnnotations0.0970.0000.103
getCores0.0000.0000.001
getTxDensity0.0150.0010.015
limitToXkb0.0730.0000.075
makeConsensusAnnotations0.0010.0010.001
metaGene0.1610.0000.161
pausingIndex0.8440.0440.898
polymeraseWave0.8990.0480.964
runMetaGene0.0140.0010.014
windowAnalysis0.2310.0130.255
writeWiggle0.2380.0200.258