BioC 3.0: CHECK report for cleanUpdTSeq on perceval

Package: cleanUpdTSeq

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cleanUpdTSeq_1.4.0.tar.gz

StartedAt: 2015-04-09 23:55:32 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-10 00:02:23 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 410.3 seconds

RetCode: 0

Status:  OK

CheckDir: cleanUpdTSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cleanUpdTSeq_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/cleanUpdTSeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cleanUpdTSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cleanUpdTSeq’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘BSgenome’ ‘BSgenome.Drerio.UCSC.danRer7’
  ‘GenomicRanges’ ‘seqinr’ ‘e1071’
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 ‘cleanUpdTSeq’ can be installed ... [30s/30s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BED2GRangesSeq: no visible global function definition for ‘IRanges’
getDownstreamSequence: no visible global function definition for
  ‘IRanges’
getDownstreamSequence: no visible global function definition for
  ‘seqlengths’
getUpstreamSequence: no visible global function definition for
  ‘IRanges’
getUpstreamSequence: no visible global function definition for
  ‘seqlengths’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [83s/85s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
data.NaiveBayes    36.017  0.640  36.733
predictTestSet     24.348  1.185  25.796
buildFeatureVector  5.155  0.060   5.408
* 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/cleanUpdTSeq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
BED2GRangesSeq	0.042	0.001	0.071
buildFeatureVector	5.155	0.060	5.408
cleanUpdTSeq-package	0.010	0.001	0.011
data.NaiveBayes	36.017	0.640	36.733
getDownstreamSequence	0.336	0.022	0.363
getUpstreamSequence	0.350	0.004	0.359
predictTestSet	24.348	1.185	25.796