BioC 3.2: CHECK report for cleanUpdTSeq on perceval

Package: cleanUpdTSeq

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.7.1.tar.gz

StartedAt: 2015-08-23 23:13:30 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:19:21 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 350.1 seconds

RetCode: 0

Status:  OK

CheckDir: cleanUpdTSeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/cleanUpdTSeq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.7.1’
* 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 ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... 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 ... [67s/67s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
data.NaiveBayes 24.896  0.649  25.630
predictTestSet  24.472  0.742  25.234
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [24s/24s]
 [24s/24s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.033	0.000	0.033
PASclassifier-class	0.057	0.017	0.074
buildClassifier	0.001	0.001	0.001
buildFeatureVector	4.621	0.027	4.656
classifier	0.051	0.012	0.063
cleanUpdTSeq-package	0.009	0.001	0.010
data.NaiveBayes	24.896	0.649	25.630
getDownstreamSequence	0.310	0.039	0.348
getUpstreamSequence	0.276	0.002	0.279
predictTestSet	24.472	0.742	25.234