BioC 3.5: CHECK report for GenomicFeatures on toluca2

Package: GenomicFeatures

Version: 1.27.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.27.15.tar.gz

StartedAt: 2017-04-23 04:26:54 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 04:42:30 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 936.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicFeatures.Rcheck

Warnings: 1

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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_1.27.15.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 r72187)
* 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 ‘1.27.15’
* 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 ... WARNING
Undocumented code objects:
  ‘exonicParts’ ‘intronicParts’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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       42.132  8.385  60.827
coordinate-mapping-methods 46.985  2.147  50.558
makeFeatureDbFromUCSC      38.051  2.279 155.831
makeTxDbFromBiomart        23.225  0.923  66.795
extractTranscriptSeqs      15.894  0.259  18.856
makeTxDbFromUCSC            7.971  0.250 108.511
makeTxDbFromGFF             7.465  0.195   7.779
transcriptLocs2refLocs      5.918  0.090   6.186
transcriptLengths           5.644  0.164   5.814
* 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: 1 WARNING, 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	0.001	0.001	0.001
FeatureDb-class	0.077	0.007	0.082
TxDb-class	2.040	0.160	2.228
as-format-methods	2.764	0.025	2.815
coordinate-mapping-methods	46.985	2.147	50.558
coverageByTranscript	42.132	8.385	60.827
disjointExons	0.001	0.000	0.000
extractTranscriptSeqs	15.894	0.259	18.856
extractUpstreamSeqs	2.027	0.252	2.761
features	0.074	0.001	0.086
getPromoterSeq-methods	0.966	0.040	1.107
id2name	0.193	0.004	0.232
makeFeatureDbFromUCSC	38.051	2.279	155.831
makeTxDb	1.506	0.059	1.591
makeTxDbFromBiomart	23.225	0.923	66.795
makeTxDbFromGFF	7.465	0.195	7.779
makeTxDbFromGRanges	3.509	0.053	3.603
makeTxDbFromUCSC	7.971	0.250	108.511
makeTxDbPackage	0.560	0.034	2.626
mapIdsToRanges	0.666	0.003	0.680
mapRangesToIds	0.968	0.005	0.984
microRNAs	0.001	0.001	0.000
nearest-methods	0.683	0.011	0.700
select-methods	0.435	0.007	0.448
transcriptLengths	5.644	0.164	5.814
transcriptLocs2refLocs	5.918	0.090	6.186
transcripts	2.546	0.025	2.606
transcriptsBy	0.833	0.011	0.848
transcriptsByOverlaps	0.173	0.002	0.178