BioC 3.2: CHECK report for GenomicFeatures on oaxaca

Package: GenomicFeatures

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.22.0.tar.gz

StartedAt: 2015-10-27 04:00:24 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:14:09 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 825.4 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 GenomicFeatures_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
  ‘AnnotationDbi’
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 ‘GenomicFeatures’ can be installed ... [19s/20s] 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
'library' or 'require' calls in package code:
  ‘FDb.UCSC.tRNAs’ ‘mirbase.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.resort’
  ‘AnnotationDbi:::.testForValidKeytype’
  ‘AnnotationDbi:::.testSelectArgs’ ‘AnnotationDbi:::.valid.colnames’
  ‘AnnotationDbi:::.valid.metadata.table’
  ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
  ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.microRNAs: no visible global function definition for ‘mirbase_dbconn’
supportedMiRBaseBuildValues: no visible global function definition for
  ‘toTable’
supportedMiRBaseBuildValues: no visible binding for global variable
  ‘mirbaseSPECIES’
* checking Rd files ... NOTE
prepare_Rd: makeTxDbFromGRanges.Rd:43-44: Dropping empty section \details
* 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 ... [212s/476s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
coverageByTranscript       48.796  9.569  58.614
coordinate-mapping-methods 47.920  2.345  61.589
makeTxDbFromBiomart        31.244  1.475 148.284
extractTranscriptSeqs      11.780  0.302  12.147
makeFeatureDbFromUCSC       9.489  0.275  98.149
makeTxDbFromUCSC            9.017  0.210  48.982
transcriptLocs2refLocs      8.858  0.158   9.109
makeTxDbFromGFF             5.160  0.172   8.850
makeTxDbFromGRanges         2.599  0.024   5.245
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [142s/155s]
 [142s/156s] 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
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.001	0.001
FeatureDb-class	0.022	0.001	0.023
TxDb-class	0.746	0.067	0.827
as-format-methods	0.883	0.006	0.890
coordinate-mapping-methods	47.920	2.345	61.589
coverageByTranscript	48.796	9.569	58.614
disjointExons	0.001	0.000	0.000
extractTranscriptSeqs	11.780	0.302	12.147
extractUpstreamSeqs	2.353	0.310	3.672
features	0.074	0.002	0.076
getPromoterSeq-methods	0.996	0.047	1.044
id2name	0.044	0.002	0.045
makeFeatureDbFromUCSC	9.489	0.275	98.149
makeTxDb	0.092	0.004	0.095
makeTxDbFromBiomart	31.244	1.475	148.284
makeTxDbFromGFF	5.160	0.172	8.850
makeTxDbFromGRanges	2.599	0.024	5.245
makeTxDbFromUCSC	9.017	0.210	48.982
makeTxDbPackage	0.375	0.006	1.259
microRNAs	0.000	0.000	0.001
nearest-methods	0.535	0.015	0.550
select-methods	0.081	0.003	0.084
transcriptLengths	3.135	0.231	3.369
transcriptLocs2refLocs	8.858	0.158	9.109
transcripts	2.429	0.053	2.486
transcriptsBy	0.892	0.006	0.899
transcriptsByOverlaps	0.112	0.001	0.113