BioC 2.14: CHECK report for GenomicFeatures on petty

Package: GenomicFeatures

Version: 1.16.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.16.3.tar.gz

StartedAt: 2014-10-07 22:11:42 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:27:37 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 955.5 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.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 GenomicFeatures_1.16.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.16.3’
* 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 ‘GenomicFeatures’ can be installed ... [40s/42s] 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘biomaRt:::martBM’
  ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘Biostrings:::.V_recycle’ ‘Biostrings:::getDNAComplementLookup’
  ‘GenomicRanges:::unsafe.extractTranscripts’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘IRanges:::duplicatedIntegerQuads’ ‘IRanges:::fancy_mseq’
  ‘IRanges:::matchIntegerQuads’ ‘IRanges:::orderIntegerQuads’
  ‘rtracklayer:::ucscTableOutputs’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [196s/337s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptSeqs       113.048  8.021 122.000
makeFeatureDbFromUCSC        14.094  0.298  93.695
makeTranscriptDbFromUCSC      8.051  0.136  50.415
transcripts                   6.551  0.032   6.655
getPromoterSeq-methods        4.608  0.529   5.189
makeTranscriptDbFromBiomart   2.069  0.095  20.366
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [194s/211s]
 [195s/211s] OK
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
DEFAULT_CIRC_SEQS	0.001	0.000	0.001
FeatureDb-class	0.066	0.003	0.071
TranscriptDb-class	1.742	0.127	1.882
as-format-methods	4.563	0.037	4.683
extractTranscriptSeqs	113.048	8.021	122.000
extractTranscriptsFromGenome	0.005	0.001	0.006
features	0.209	0.006	0.215
getPromoterSeq-methods	4.608	0.529	5.189
id2name	0.128	0.005	0.136
makeFeatureDbFromUCSC	14.094	0.298	93.695
makeTranscriptDb	0.212	0.007	0.220
makeTranscriptDbFromBiomart	2.069	0.095	20.366
makeTranscriptDbFromGFF	3.410	0.046	3.472
makeTranscriptDbFromUCSC	8.051	0.136	50.415
makeTxDbPackage	0.907	0.020	0.940
nearest-methods	2.778	0.038	2.867
saveFeatures	0.002	0.000	0.001
select-methods	0.469	0.011	0.482
transcripts	6.551	0.032	6.655
transcriptsBy	3.724	0.025	3.757
transcriptsByOverlaps	0.690	0.005	0.695