BioC 3.2: CHECK report for GenomicFeatures on linux1.bioconductor.org

Package: GenomicFeatures

Version: 1.22.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.22.0.tar.gz

StartedAt: 2015-10-27 03:55:35 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:07:11 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 695.5 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GenomicFeatures.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 ‘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 ... [17s/17s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [171s/409s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
coverageByTranscript       44.873  1.439  46.401
coordinate-mapping-methods 37.270  0.711  40.176
makeTxDbFromBiomart        24.288  0.166 102.180
extractTranscriptSeqs      11.199  0.021  11.229
makeFeatureDbFromUCSC       9.926  0.043 115.900
makeTxDbFromUCSC            8.216  0.065  60.391
transcriptLocs2refLocs      7.434  0.004   7.455
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [123s/129s]
 [123s/129s] 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
  ‘/home/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	0	0
FeatureDb-class	0.015	0.000	0.014
TxDb-class	0.556	0.047	0.604
as-format-methods	0.910	0.003	0.915
coordinate-mapping-methods	37.270	0.711	40.176
coverageByTranscript	44.873	1.439	46.401
disjointExons	0.001	0.000	0.001
extractTranscriptSeqs	11.199	0.021	11.229
extractUpstreamSeqs	1.720	0.016	1.840
features	0.038	0.000	0.038
getPromoterSeq-methods	0.795	0.008	0.804
id2name	0.046	0.000	0.046
makeFeatureDbFromUCSC	9.926	0.043	115.900
makeTxDb	0.091	0.000	0.091
makeTxDbFromBiomart	24.288	0.166	102.180
makeTxDbFromGFF	3.823	0.004	3.998
makeTxDbFromGRanges	2.897	0.004	2.904
makeTxDbFromUCSC	8.216	0.065	60.391
makeTxDbPackage	0.331	0.004	0.338
microRNAs	0.001	0.000	0.001
nearest-methods	0.623	0.004	0.627
select-methods	0.127	0.004	0.131
transcriptLengths	3.296	0.004	3.307
transcriptLocs2refLocs	7.434	0.004	7.455
transcripts	1.561	0.007	1.568
transcriptsBy	0.561	0.000	0.561
transcriptsByOverlaps	0.063	0.004	0.066