BioC 3.1: CHECK report for cleanUpdTSeq on zin2

Package: cleanUpdTSeq

Version: 1.6.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.6.1.tar.gz

StartedAt: 2015-10-08 23:34:03 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:38:03 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 239.1 seconds

RetCode: 0

Status:  OK

CheckDir: cleanUpdTSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cleanUpdTSeq_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/cleanUpdTSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.1’
* 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 ... [12s/15s] 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 ... [48s/59s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
predictTestSet  20.825  0.078  25.610
data.NaiveBayes 17.135  0.246  21.689
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [14s/18s]
 [14s/18s] 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/cleanUpdTSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘cleanUpdTSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cleanUpdTSeq)

name	user	system	elapsed
BED2GRangesSeq	0.030	0.000	0.029
PASclassifier-class	0.042	0.000	0.054
buildClassifier	0.001	0.000	0.000
buildFeatureVector	3.623	0.017	4.091
classifier	0.04	0.00	0.04
cleanUpdTSeq-package	0.004	0.000	0.004
data.NaiveBayes	17.135	0.246	21.689
getDownstreamSequence	0.229	0.012	0.455
getUpstreamSequence	0.196	0.000	0.236
predictTestSet	20.825	0.078	25.610