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CHECK report for macat on merida1

This page was generated on 2019-04-16 11:54:12 -0400 (Tue, 16 Apr 2019).

Package 861/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
macat 1.56.0
Joern Toedling
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/macat
Branch: RELEASE_3_8
Last Commit: 36a51df
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: macat
Version: 1.56.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:macat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings macat_1.56.0.tar.gz
StartedAt: 2019-04-16 00:57:29 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:59:24 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 115.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: macat.Rcheck
Warnings: 2

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:macat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings macat_1.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/macat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘macat/DESCRIPTION’ ... OK
* this is package ‘macat’ version ‘1.56.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘macat’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /Users/biocbuild/bbs-3.8-bioc/meat/macat/man/loaddatapkg.Rd:24: unexpected '}'
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/macat.Rcheck/00install.out’ for details.
* 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 ... NOTE
'library' or 'require' call to ‘annotate’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘annotate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘annotate:::getTDRows’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalScoring : computePermSlideScores: warning in compute.sliding(permM,
  chrom = chromosome, sample = 1, kernel, kernelparams, step.width =
  step.width): partial argument match of 'chrom' to 'chromosome'
preprocessedLoader: warning in require(chip, character.only = TRUE,
  quiet = TRUE): partial argument match of 'quiet' to 'quietly'
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
buildMACAT: no visible global function definition for ‘featureNames’
buildMACAT: no visible global function definition for ‘sampleNames’
buildMACAT: no visible global function definition for ‘exprs’
compare.gammas: no visible global function definition for ‘x11’
compare.gammas: no visible global function definition for ‘lines’
compare.gammas: no visible global function definition for ‘legend’
discreteKernelize: no visible binding for global variable ‘quantile’
discretize: no visible binding for global variable ‘quantile’
discretizeChromosome: no visible binding for global variable ‘quantile’
discretizeOne: no visible binding for global variable ‘quantile’
evalScoring: no visible binding for global variable ‘quantile’
getHtml: no visible global function definition for ‘browseURL’
loaddatapkg: no visible global function definition for
  ‘install.packages’
loaddatapkg: no visible global function definition for ‘contrib.url’
plot.MACATevalScoring: no visible global function definition for ‘x11’
plot.MACATevalScoring: no visible global function definition for ‘png’
plot.MACATevalScoring: no visible global function definition for ‘par’
plot.MACATevalScoring: no visible global function definition for
  ‘points’
plot.MACATevalScoring: no visible global function definition for
  ‘lines’
plot.MACATevalScoring: no visible global function definition for
  ‘title’
plot.MACATevalScoring: no visible global function definition for ‘axis’
plot.MACATevalScoring: no visible global function definition for
  ‘mtext’
plot.MACATevalScoring: no visible global function definition for
  ‘dev.off’
plotSliding: no visible global function definition for ‘lines’
preprocessedLoader: no visible global function definition for
  ‘read.delim’
preprocessedLoader: no visible global function definition for
  ‘read.table’
preprocessedLoader: no visible global function definition for
  ‘buildChromLocation’
preprocessedLoader: no visible global function definition for ‘new’
preprocessedLoader: no visible global function definition for ‘pData<-’
preprocessedLoader: no visible global function definition for
  ‘varLabels<-’
preprocessedLoader: no visible global function definition for
  ‘chromLocs’
preprocessedLoader : usedChromGenes2: no visible global function
  definition for ‘chromLocs’
preprocessedLoader : usedChromGenes2: no visible global function
  definition for ‘featureNames’
scoring : tscore: no visible global function definition for ‘median’
scoring : tscoremat: no visible binding for global variable ‘median’
scoring : pval: no visible binding for global variable ‘pt’
scoring: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  addVigs2WinMenu axis browseURL buildChromLocation chromLocs
  contrib.url dev.off exprs featureNames install.packages legend lines
  median mtext new pData<- par png points pt quantile read.delim
  read.table sampleNames title varLabels<- x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "x11")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "points", "title")
  importFrom("methods", "new")
  importFrom("stats", "median", "pt", "quantile")
  importFrom("utils", "browseURL", "contrib.url", "install.packages",
             "read.delim", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: loaddatapkg.Rd:24: unexpected '}'
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 21.465  0.125  21.783
get_results         9.794  0.032   9.912
* 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 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/macat.Rcheck/00check.log’
for details.



Installation output

macat.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL macat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘macat’ ...
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: /Users/biocbuild/bbs-3.8-bioc/meat/macat/man/loaddatapkg.Rd:24: unexpected '}'
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (macat)

Tests output


Example timings

macat.Rcheck/macat-Ex.timings

nameusersystemelapsed
buildMACAT1.1780.1141.303
compute_sliding1.6300.0071.651
discreteKernelize1.5320.0061.550
discretizeAll000
discretize_tscores21.465 0.12521.783
evalScoring2.7430.0842.853
evaluateParameters0.5420.0230.570
get_results9.7940.0329.912
kernelize0.4900.0020.497
kernelizeAll000
kernelizeToPython000
kernels0.0190.0020.020
loaddatapkg000
plot_MACATevalScoring000
preprocessedLoader0.0010.0000.000
pythondata000
scoring0.0160.0010.017
stjd0.0130.0020.016