GenomicFeatures 1.23.4
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicFeatures | | Last Changed Rev: 109858 / Revision: 109948 | | Last Changed Date: 2015-10-23 00:47:11 -0400 (Fri, 23 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.23.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicFeatures.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.23.4’
* 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 ... [14s/14s] 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’
Undefined global functions or variables:
mirbaseSPECIES mirbase_dbconn toTable
* checking Rd files ... NOTE
prepare_Rd: makeTxDbFromGRanges.Rd:43-44: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'transcriptsByOverlaps.Rd':
‘[IRanges:IntervalTree-class]{findOverlaps}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... [3m/12m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
coverageByTranscript 37.846 1.104 38.984
coordinate-mapping-methods 35.844 0.672 36.792
makeTxDbFromBiomart 27.144 0.169 108.333
extractTranscriptSeqs 9.063 0.004 9.074
makeFeatureDbFromUCSC 8.448 0.051 447.097
makeTxDbFromUCSC 8.128 0.032 68.459
transcriptLocs2refLocs 5.550 0.000 5.551
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘GenomicFeatures_unit_tests.R’ [122s/128s]
[122s/128s] 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.