BioC 3.4: CHECK report for GenomicFeatures on malbec1

Package: GenomicFeatures

Version: 1.26.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.26.4.tar.gz

StartedAt: 2017-04-14 22:47:34 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:00:33 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 779.0 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_1.26.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.26.4’
* 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 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 38.040  1.716  39.956
coverageByTranscript       34.008  3.668  37.719
makeFeatureDbFromUCSC      25.480  0.340 142.664
makeTxDbFromBiomart        16.244  0.220  71.688
extractTranscriptSeqs       9.700  0.036   9.745
makeTxDbFromUCSC            6.460  0.292 139.508
* 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	0.000	0.000	0.001
FeatureDb-class	0.028	0.000	0.028
TxDb-class	1.260	0.044	1.305
as-format-methods	0.812	0.012	0.826
coordinate-mapping-methods	38.040	1.716	39.956
coverageByTranscript	34.008	3.668	37.719
disjointExons	0	0	0
extractTranscriptSeqs	9.700	0.036	9.745
extractUpstreamSeqs	1.436	0.032	1.570
features	0.048	0.000	0.050
getPromoterSeq-methods	0.892	0.000	0.895
id2name	0.096	0.000	0.094
makeFeatureDbFromUCSC	25.480	0.340	142.664
makeTxDb	0.084	0.000	0.084
makeTxDbFromBiomart	16.244	0.220	71.688
makeTxDbFromGFF	3.244	0.016	3.346
makeTxDbFromGRanges	2.600	0.000	2.624
makeTxDbFromUCSC	6.460	0.292	139.508
makeTxDbPackage	0.332	0.004	2.781
mapIdsToRanges	0.700	0.012	0.711
mapRangesToIds	0.720	0.000	0.721
microRNAs	0	0	0
nearest-methods	0.556	0.000	0.554
select-methods	0.148	0.000	0.146
transcriptLengths	4.556	0.032	4.592
transcriptLocs2refLocs	4.220	0.012	4.234
transcripts	2.156	0.004	2.163
transcriptsBy	0.752	0.000	0.753
transcriptsByOverlaps	0.100	0.000	0.104