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BioC 3.0: CHECK report for macat on oaxaca

This page was generated on 2015-04-10 10:01:31 -0700 (Fri, 10 Apr 2015).

Package 498/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
macat 1.40.0
Joern Toedling
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/macat
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: macat
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.40.0.tar.gz
StartedAt: 2015-04-10 00:54:19 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:57:24 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 185.8 seconds
RetCode: 0
Status:  OK 
CheckDir: macat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/macat.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘macat/DESCRIPTION’ ... OK
* this is package ‘macat’ version ‘1.40.0’
* 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 ... [12s/12s] 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 loading without being on the library search path ... 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’
preprocessedLoader: no visible global function definition for
  ‘buildChromLocation’
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’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [67s/70s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 33.397  0.121  34.875
get_results        14.739  0.046  15.608
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/macat.Rcheck/00check.log’
for details.

macat.Rcheck/00install.out:

* installing *source* package ‘macat’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (macat)

macat.Rcheck/macat-Ex.timings:

nameusersystemelapsed
buildMACAT3.2690.0613.467
compute_sliding2.5430.0062.610
discreteKernelize2.1000.0052.120
discretizeAll0.0010.0000.000
discretize_tscores33.397 0.12134.875
evalScoring3.3320.0943.498
evaluateParameters0.7860.0320.822
get_results14.739 0.04615.608
kernelize0.6350.0010.760
kernelizeAll0.0010.0000.001
kernelizeToPython0.0010.0000.001
kernels0.0240.0020.025
loaddatapkg0.0010.0000.000
plot_MACATevalScoring0.0010.0000.001
preprocessedLoader0.0010.0000.001
pythondata0.0010.0000.001
scoring0.0230.0010.023
stjd0.0180.0000.018