BioC 3.4: CHECK report for GenomicFeatures on morelia

Package: GenomicFeatures

Version: 1.25.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.25.16.tar.gz

StartedAt: 2016-09-20 07:06:57 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:18:50 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 713.0 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_1.25.16.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.25.16’
* 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
coordinate-mapping-methods 43.096  2.140  47.640
coverageByTranscript       32.492  8.416  40.994
makeFeatureDbFromUCSC      25.995  1.586 126.385
makeTxDbFromBiomart        13.735  0.890  68.807
extractTranscriptSeqs       9.556  0.094   9.739
makeTxDbFromUCSC            5.278  0.199 101.430
makeTxDbFromGFF             5.043  0.141   5.333
TxDb-class                  0.772  0.076  11.906
* 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
  ‘/Users/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	0.000	0.000	0.001
FeatureDb-class	0.015	0.001	0.016
TxDb-class	0.772	0.076	11.906
as-format-methods	0.872	0.026	0.898
coordinate-mapping-methods	43.096	2.140	47.640
coverageByTranscript	32.492	8.416	40.994
disjointExons	0	0	0
extractTranscriptSeqs	9.556	0.094	9.739
extractUpstreamSeqs	1.284	0.192	2.878
features	0.032	0.001	0.033
getPromoterSeq-methods	0.525	0.035	0.576
id2name	0.068	0.002	0.070
makeFeatureDbFromUCSC	25.995	1.586	126.385
makeTxDb	0.104	0.003	0.107
makeTxDbFromBiomart	13.735	0.890	68.807
makeTxDbFromGFF	5.043	0.141	5.333
makeTxDbFromGRanges	2.379	0.026	2.406
makeTxDbFromUCSC	5.278	0.199	101.430
makeTxDbPackage	0.350	0.024	1.780
mapIdsToRanges	0.358	0.002	0.360
mapRangesToIds	0.581	0.002	0.584
microRNAs	0	0	0
nearest-methods	0.380	0.005	0.384
select-methods	0.082	0.003	0.084
transcriptLengths	2.407	0.162	2.569
transcriptLocs2refLocs	4.361	0.080	4.501
transcripts	1.439	0.014	1.453
transcriptsBy	0.674	0.008	0.682
transcriptsByOverlaps	0.156	0.002	0.159