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BioC 3.2: CHECK report for biomaRt on zin1

This page was generated on 2015-08-24 10:47:00 -0700 (Mon, 24 Aug 2015).

Package 102/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.25.1
Steffen Durinck
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biomaRt
Last Changed Rev: 102837 / Revision: 107696
Last Changed Date: 2015-04-20 10:13:20 -0700 (Mon, 20 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biomaRt
Version: 2.25.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biomaRt_2.25.1.tar.gz
StartedAt: 2015-08-23 22:01:37 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 22:02:47 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 69.4 seconds
RetCode: 0
Status:  OK 
CheckDir: biomaRt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings biomaRt_2.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/biomaRt.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.25.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘biomaRt’ can be installed ... [6s/7s] 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 object imported by a ':::' call: ‘AnnotationDbi:::smartKeys’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.keys’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/6s] 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 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/biomaRt.Rcheck/00check.log’
for details.


biomaRt.Rcheck/00install.out:

* installing *source* package ‘biomaRt’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomaRt)

biomaRt.Rcheck/biomaRt-Ex.timings:

nameusersystemelapsed
NP2009code0.0000.0000.001
attributePages0.0010.0000.000
exportFASTA0.0010.0000.001
filterOptions0.0010.0000.001
filterType0.0000.0000.001
getBM0.0010.0000.001
getBMlist0.0010.0000.000
getGene0.0010.0000.002
getLDS0.0010.0000.000
getSequence0.0020.0000.001
getXML0.0000.0000.001
listAttributes0.0010.0000.000
listDatasets0.0000.0000.001
listEnsembl0.0010.0000.001
listFilters0.0000.0000.001
listMarts0.0010.0000.001
select0.1210.0202.458
useDataset0.0010.0000.001
useEnsembl0.0010.0000.001
useMart000