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BioC 3.2: CHECK report for macat on oaxaca

This page was generated on 2016-04-23 10:22:58 -0700 (Sat, 23 Apr 2016).

Package 581/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
macat 1.44.1
Joern Toedling
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/macat
Last Changed Rev: 112152 / Revision: 116712
Last Changed Date: 2016-01-04 13:42:06 -0800 (Mon, 04 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: macat
Version: 1.44.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings macat_1.44.1.tar.gz
StartedAt: 2016-04-23 01:39:20 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:41:28 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 127.9 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 macat_1.44.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/macat.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.44.1’
* 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 ... [8s/8s] 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 ... [49s/50s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 23.352  0.079  23.464
get_results        10.541  0.023  10.575
* 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
  ‘/Users/biocbuild/bbs-3.2-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
buildMACAT3.1190.0533.286
compute_sliding1.7550.0121.795
discreteKernelize1.5580.0071.569
discretizeAll0.0010.0000.001
discretize_tscores23.352 0.07923.464
evalScoring3.1720.0863.260
evaluateParameters0.7530.0230.777
get_results10.541 0.02310.575
kernelize0.4880.0020.490
kernelizeAll0.0000.0000.001
kernelizeToPython0.0000.0010.001
kernels0.0190.0010.021
loaddatapkg000
plot_MACATevalScoring0.0010.0000.000
preprocessedLoader000
pythondata0.0010.0000.001
scoring0.0210.0020.023
stjd0.0170.0020.018