BioC 2.13: CHECK report for GenomicFeatures on perceval

Package: GenomicFeatures

Version: 1.14.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.14.5.tar.gz

StartedAt: 2014-04-05 01:34:06 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:47:12 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 786.1 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.14.5’
* 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 ... [28s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘rtracklayer’ ‘biomaRt’ ‘Biostrings’
A package should be listed in only one of these fields.
* 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
‘:::’ calls which should be ‘::’:
  ‘DBI:::dbGetQuery’ ‘DBI:::dbListFields’ ‘DBI:::dbListTables’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘Biostrings:::getDNAComplementLookup’
  ‘rtracklayer:::ucscTableOutputs’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.keys’ ‘.reverseColAbbreviations’
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 ... NOTE
.setseqnameStyle: no visible binding for global variable ‘txdb’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GenomicFeatures.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [180s/317s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 99.996 22.779 125.908
makeFeatureDbFromUCSC        10.568  0.501  86.448
makeTranscriptDbFromUCSC      7.222  0.193  48.886
makeTranscriptDbFromBiomart   2.354  0.235  18.475
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [162s/179s]
 [162s/180s] 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 were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.538	0.004	0.547
FeatureDb-class	0.055	0.007	0.063
TranscriptDb-class	1.523	0.261	1.871
as-format-methods	2.411	0.036	2.452
extractTranscriptsFromGenome	99.996	22.779	125.908
features	0.133	0.014	0.148
getPromoterSeq-methods	3.226	0.700	3.986
id2name	0.157	0.067	0.225
makeFeatureDbFromUCSC	10.568	0.501	86.448
makeTranscriptDb	0.109	0.014	0.127
makeTranscriptDbFromBiomart	2.354	0.235	18.475
makeTranscriptDbFromGFF	2.423	0.106	2.557
makeTranscriptDbFromUCSC	7.222	0.193	48.886
makeTxDbPackage	0.677	0.040	0.749
nearest-methods	1.715	0.051	1.845
saveFeatures	0.002	0.005	0.007
select-methods	0.300	0.030	0.332
transcripts	3.937	0.044	3.997
transcriptsBy	2.751	0.034	2.862
transcriptsByOverlaps	0.525	0.012	0.537