BioC 3.2: CHECK report for GenomicFeatures on perceval

Package: GenomicFeatures

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.22.0.tar.gz

StartedAt: 2015-10-27 08:13:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:27:57 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 877.6 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.22.0’
* 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 ... [22s/22s] 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
'library' or 'require' calls in package code:
  ‘FDb.UCSC.tRNAs’ ‘mirbase.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.resort’
  ‘AnnotationDbi:::.testForValidKeytype’
  ‘AnnotationDbi:::.testSelectArgs’ ‘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 ... NOTE
.microRNAs: no visible global function definition for ‘mirbase_dbconn’
supportedMiRBaseBuildValues: no visible global function definition for
  ‘toTable’
supportedMiRBaseBuildValues: no visible binding for global variable
  ‘mirbaseSPECIES’
* checking Rd files ... NOTE
prepare_Rd: makeTxDbFromGRanges.Rd:43-44: Dropping empty section \details
* 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 ... [249s/490s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
coverageByTranscript       57.406 13.496  70.907
coordinate-mapping-methods 54.022  3.431  59.545
makeTxDbFromBiomart        37.944  2.178 155.788
extractTranscriptSeqs      12.606  0.180  12.864
makeFeatureDbFromUCSC      11.444  0.756  97.503
makeTxDbFromUCSC           10.450  0.238  47.825
transcriptLocs2refLocs      9.751  0.248   9.999
makeTxDbFromGFF             5.957  0.229   6.474
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [162s/175s]
 [163s/175s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.000	0.001
FeatureDb-class	0.025	0.001	0.027
TxDb-class	0.761	0.090	0.852
as-format-methods	0.899	0.010	0.909
coordinate-mapping-methods	54.022	3.431	59.545
coverageByTranscript	57.406	13.496	70.907
disjointExons	0.001	0.000	0.000
extractTranscriptSeqs	12.606	0.180	12.864
extractUpstreamSeqs	2.713	0.323	3.956
features	0.081	0.001	0.082
getPromoterSeq-methods	1.194	0.048	1.241
id2name	0.043	0.002	0.045
makeFeatureDbFromUCSC	11.444	0.756	97.503
makeTxDb	0.088	0.005	0.092
makeTxDbFromBiomart	37.944	2.178	155.788
makeTxDbFromGFF	5.957	0.229	6.474
makeTxDbFromGRanges	2.808	0.027	2.835
makeTxDbFromUCSC	10.450	0.238	47.825
makeTxDbPackage	0.437	0.005	0.479
microRNAs	0.001	0.000	0.001
nearest-methods	0.643	0.024	0.667
select-methods	0.125	0.004	0.129
transcriptLengths	4.102	0.273	4.374
transcriptLocs2refLocs	9.751	0.248	9.999
transcripts	2.112	0.083	2.194
transcriptsBy	0.871	0.006	0.878
transcriptsByOverlaps	0.337	0.001	0.338