BioC 3.0: CHECK report for macat on zin1

Package: macat

Version: 1.40.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings macat_1.40.0.tar.gz

StartedAt: 2015-04-10 01:31:53 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:34:17 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 144.4 seconds

RetCode: 0

Status:  OK

CheckDir: macat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings macat_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/macat.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [10s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/56s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 28.194  0.028  28.644
get_results        12.521  0.000  12.554
* 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/macat.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
buildMACAT	1.680	0.028	1.743
compute_sliding	2.148	0.004	2.159
discreteKernelize	1.848	0.000	1.851
discretizeAll	0.000	0.000	0.001
discretize_tscores	28.194	0.028	28.644
evalScoring	2.932	0.024	2.973
evaluateParameters	0.740	0.012	0.755
get_results	12.521	0.000	12.554
kernelize	0.552	0.000	0.555
kernelizeAll	0.000	0.000	0.001
kernelizeToPython	0	0	0
kernels	0.020	0.000	0.019
loaddatapkg	0	0	0
plot_MACATevalScoring	0.000	0.000	0.001
preprocessedLoader	0.004	0.000	0.000
pythondata	0	0	0
scoring	0.02	0.00	0.02
stjd	0.016	0.000	0.014