BioC 3.5: CHECK report for GenomicFeatures on oaxaca

Package: GenomicFeatures

Version: 1.27.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.27.9.tar.gz

StartedAt: 2017-03-04 03:29:47 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:53:00 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 1392.7 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_1.27.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomicFeatures.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.27.9’
* 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:
  ‘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       43.772 10.152  56.608
coordinate-mapping-methods 49.274  2.258  55.070
makeFeatureDbFromUCSC      33.057  2.079 572.047
extractTranscriptSeqs      16.972  0.206  18.845
makeTxDbFromBiomart        15.163  0.819  83.189
makeTxDbFromUCSC            7.840  0.235 130.901
transcriptLocs2refLocs      5.919  0.086   6.870
transcriptLengths           5.604  0.143   5.751
makeTxDbFromGFF             4.642  0.102   6.448
* 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-3.5-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	0.077	0.006	0.084
TxDb-class	1.874	0.115	2.054
as-format-methods	2.462	0.018	2.482
coordinate-mapping-methods	49.274	2.258	55.070
coverageByTranscript	43.772	10.152	56.608
disjointExons	0.000	0.000	0.001
extractTranscriptSeqs	16.972	0.206	18.845
extractUpstreamSeqs	2.341	0.274	3.853
features	0.078	0.002	0.080
getPromoterSeq-methods	1.082	0.082	1.498
id2name	0.232	0.005	0.238
makeFeatureDbFromUCSC	33.057	2.079	572.047
makeTxDb	2.574	0.125	2.700
makeTxDbFromBiomart	15.163	0.819	83.189
makeTxDbFromGFF	4.642	0.102	6.448
makeTxDbFromGRanges	3.178	0.066	4.484
makeTxDbFromUCSC	7.840	0.235	130.901
makeTxDbPackage	0.549	0.018	3.111
mapIdsToRanges	0.845	0.004	0.865
mapRangesToIds	0.910	0.006	0.916
microRNAs	0	0	0
nearest-methods	0.884	0.012	0.935
select-methods	0.232	0.005	0.236
transcriptLengths	5.604	0.143	5.751
transcriptLocs2refLocs	5.919	0.086	6.870
transcripts	2.546	0.025	2.573
transcriptsBy	0.838	0.008	2.441
transcriptsByOverlaps	0.193	0.002	0.196