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BioC 3.4: CHECK report for OrganismDbi on malbec1

This page was generated on 2017-04-15 16:11:04 -0400 (Sat, 15 Apr 2017).

Package 875/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrganismDbi 1.16.0
Biocore Data Team
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/OrganismDbi
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OrganismDbi
Version: 1.16.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.16.0.tar.gz
StartedAt: 2017-04-15 00:15:57 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:26:01 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 603.8 seconds
RetCode: 0
Status:  OK 
CheckDir: OrganismDbi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/OrganismDbi.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 ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.16.0’
* 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 ‘OrganismDbi’ 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 object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  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:
  ‘.biocAnnPackages’ ‘.extractPkgsAndCols’ ‘.gentlyExtractDbFiles’
  ‘.lookupDbNameFromKeytype’ ‘.mungeGraphData’ ‘.taxIdToOrgDb’
  ‘.taxIdToOrgDbName’ ‘.testGraphData’ ‘.testKeys’ ‘OrganismDb’
* 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
makeOrganismDbFromBiomart 14.032  0.192  37.711
OrganismDb                10.048  0.092  12.659
rangeBasedAccessors        7.056  0.012   7.070
makeOrganismDbFromUCSC     4.980  0.068  80.238
makeOrganismDbFromTxDb     4.528  0.096  77.058
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘OrganismDbi_unit_tests.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.


OrganismDbi.Rcheck/00install.out:

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

OrganismDbi.Rcheck/OrganismDbi-Ex.timings:

nameusersystemelapsed
OrganismDb10.048 0.09212.659
coordinate-mapping-method0.6960.0080.703
makeOrganismDbFromBiomart14.032 0.19237.711
makeOrganismDbFromTxDb 4.528 0.09677.058
makeOrganismDbFromUCSC 4.980 0.06880.238
makeOrganismPackage0.0000.0000.001
rangeBasedAccessors7.0560.0127.070