BioC 2.14: CHECK report for GenomicFeatures on zin2

Package: GenomicFeatures

Version: 1.16.3

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.16.3.tar.gz

StartedAt: 2014-10-07 23:54:28 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-08 00:03:34 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 546.1 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.16.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ... [18s/19s] 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’ ‘Biostrings:::.V_recycle’
  ‘Biostrings:::getDNAComplementLookup’
  ‘GenomicRanges:::unsafe.extractTranscripts’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘IRanges:::duplicatedIntegerQuads’ ‘IRanges:::fancy_mseq’
  ‘IRanges:::matchIntegerQuads’ ‘IRanges:::orderIntegerQuads’
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [94s/252s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
extractTranscriptSeqs       58.760  2.580  61.783
makeFeatureDbFromUCSC        5.708  0.064  83.268
makeTranscriptDbFromUCSC     2.804  0.004  46.748
makeTranscriptDbFromBiomart  0.976  0.012  35.803
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [89s/112s]
 [89s/112s] 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
  ‘/home/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	0.000	0.000	0.001
FeatureDb-class	0.032	0.000	0.034
TranscriptDb-class	0.916	0.052	0.989
as-format-methods	2.064	0.004	2.071
extractTranscriptSeqs	58.760	2.580	61.783
extractTranscriptsFromGenome	0.004	0.000	0.004
features	0.092	0.000	0.093
getPromoterSeq-methods	2.156	0.112	2.271
id2name	0.060	0.000	0.058
makeFeatureDbFromUCSC	5.708	0.064	83.268
makeTranscriptDb	0.072	0.000	0.076
makeTranscriptDbFromBiomart	0.976	0.012	35.803
makeTranscriptDbFromGFF	1.537	0.004	1.542
makeTranscriptDbFromUCSC	2.804	0.004	46.748
makeTxDbPackage	0.344	0.004	0.358
nearest-methods	1.260	0.004	1.270
saveFeatures	0.000	0.000	0.001
select-methods	0.220	0.000	0.226
transcripts	2.980	0.008	3.011
transcriptsBy	1.616	0.000	1.619
transcriptsByOverlaps	0.296	0.000	0.297