BioC 3.4: CHECK report for GenomicFeatures on morelia

Package: GenomicFeatures

Version: 1.26.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.26.4.tar.gz

StartedAt: 2017-04-15 02:43:58 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:58:13 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 855.3 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_1.26.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.26.4’
* 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
coordinate-mapping-methods 51.649  2.726  61.082
coverageByTranscript       39.407  9.563  50.608
makeFeatureDbFromUCSC      36.261  1.963 133.946
makeTxDbFromBiomart        18.475  0.966  75.961
extractTranscriptSeqs      12.306  0.116  13.675
makeTxDbFromUCSC            6.788  0.227  97.591
makeTxDbFromGFF             5.542  0.183   5.869
transcriptLengths           5.513  0.147   5.665
transcriptLocs2refLocs      5.516  0.120   5.687
* 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	0.001	0.001
FeatureDb-class	0.041	0.006	0.047
TxDb-class	1.522	0.095	1.621
as-format-methods	1.072	0.051	1.125
coordinate-mapping-methods	51.649	2.726	61.082
coverageByTranscript	39.407	9.563	50.608
disjointExons	0.001	0.000	0.000
extractTranscriptSeqs	12.306	0.116	13.675
extractUpstreamSeqs	1.832	0.244	3.316
features	0.054	0.001	0.055
getPromoterSeq-methods	0.818	0.057	1.058
id2name	0.136	0.003	0.139
makeFeatureDbFromUCSC	36.261	1.963	133.946
makeTxDb	0.132	0.004	0.135
makeTxDbFromBiomart	18.475	0.966	75.961
makeTxDbFromGFF	5.542	0.183	5.869
makeTxDbFromGRanges	3.654	0.029	3.687
makeTxDbFromUCSC	6.788	0.227	97.591
makeTxDbPackage	0.534	0.014	1.904
mapIdsToRanges	0.597	0.004	0.602
mapRangesToIds	0.837	0.003	0.840
microRNAs	0.000	0.000	0.001
nearest-methods	0.668	0.006	0.675
select-methods	0.232	0.005	0.237
transcriptLengths	5.513	0.147	5.665
transcriptLocs2refLocs	5.516	0.120	5.687
transcripts	2.287	0.018	2.307
transcriptsBy	0.971	0.009	0.981
transcriptsByOverlaps	0.311	0.003	0.313