BioC 3.4: CHECK report for GenomicFeatures on zin1

Package: GenomicFeatures

Version: 1.25.16

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.25.16.tar.gz

StartedAt: 2016-09-20 07:03:22 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:14:49 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 686.8 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFeatures.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.25.16.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.25.16’
* package encoding: UTF-8
* 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 ... 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:
  ‘AnnotationDbi:::.getMetaValue’ ‘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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
coverageByTranscript       29.808  7.072  39.108
coordinate-mapping-methods 32.608  3.132  36.152
makeFeatureDbFromUCSC      21.220  0.704 121.420
makeTxDbFromBiomart        14.816  0.252  80.755
extractTranscriptSeqs       9.948  0.040  10.151
makeTxDbFromUCSC            6.092  0.304 105.484
transcriptLocs2refLocs      5.508  0.044   5.728
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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	0.016	0.000	0.016
TxDb-class	0.764	0.040	0.802
as-format-methods	0.992	0.016	1.007
coordinate-mapping-methods	32.608	3.132	36.152
coverageByTranscript	29.808	7.072	39.108
disjointExons	0.000	0.000	0.001
extractTranscriptSeqs	9.948	0.040	10.151
extractUpstreamSeqs	1.152	0.040	1.584
features	0.036	0.000	0.035
getPromoterSeq-methods	0.556	0.000	0.554
id2name	0.072	0.004	0.076
makeFeatureDbFromUCSC	21.220	0.704	121.420
makeTxDb	0.068	0.000	0.070
makeTxDbFromBiomart	14.816	0.252	80.755
makeTxDbFromGFF	3.836	0.004	3.981
makeTxDbFromGRanges	2.748	0.004	2.754
makeTxDbFromUCSC	6.092	0.304	105.484
makeTxDbPackage	0.484	0.016	2.067
mapIdsToRanges	0.648	0.004	0.651
mapRangesToIds	0.904	0.004	0.909
microRNAs	0	0	0
nearest-methods	0.532	0.004	0.537
select-methods	0.108	0.000	0.106
transcriptLengths	3.120	0.052	3.196
transcriptLocs2refLocs	5.508	0.044	5.728
transcripts	2.192	0.008	2.198
transcriptsBy	0.684	0.004	0.686
transcriptsByOverlaps	0.092	0.000	0.094