GenomicFeatures 1.21.18
Bioconductor Package Maintainer
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 107563 / Revision: 107696 | | Last Changed Date: 2015-08-18 15:57:24 -0700 (Tue, 18 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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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_1.21.18.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.21.18’
* 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 ... [17s/18s] 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 ... [174s/409s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
coordinate-mapping-methods 53.062 2.427 64.105
makeTxDbFromBiomart 33.038 1.505 146.896
extractTranscriptSeqs 14.212 0.088 15.538
makeFeatureDbFromUCSC 10.855 0.320 78.369
transcriptLocs2refLocs 10.028 0.180 10.552
makeTxDbFromUCSC 9.838 0.236 45.638
makeTxDbFromGFF 6.667 0.242 8.560
transcriptLengths 4.556 0.398 5.098
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘GenomicFeatures_unit_tests.R’ [145s/206s]
[146s/206s] 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.