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BioC 3.2: CHECK report for OrganismDbi on zin1

This page was generated on 2015-08-24 10:48:55 -0700 (Mon, 24 Aug 2015).

Package 713/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrganismDbi 1.11.42
Biocore Data Team
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OrganismDbi
Last Changed Rev: 105883 / Revision: 107696
Last Changed Date: 2015-07-07 11:35:41 -0700 (Tue, 07 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: OrganismDbi
Version: 1.11.42
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.11.42.tar.gz
StartedAt: 2015-08-24 02:20:45 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:29:33 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 528.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: OrganismDbi.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.11.42.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/OrganismDbi.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 ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.11.42’
* 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 ... [15s/15s] 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 ... WARNING
'library' or 'require' call not declared from: ‘AnnotationHub’
'library' or 'require' call to ‘GenomicFeatures’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘AnnotationHub’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.chooseCentralOrgPkgSymbol’
  ‘AnnotationDbi:::.mapIds’ ‘AnnotationDbi:::.resort’
  ‘AnnotationDbi:::.testForValidKeytype’
  ‘AnnotationDbi:::.testSelectArgs’ ‘BiocGenerics:::testPackage’
  ‘GenomicFeatures:::.makePackageName’
  ‘GenomicFeatures:::.set.group.names’
  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 ... NOTE
.selectByRanges: no visible global function definition for
  ‘findOverlaps’
.selectByRanges: no visible global function definition for ‘queryHits’
.selectByRanges: no visible global function definition for
  ‘subjectHits’
.taxIdToOrgDb: no visible global function definition for
  ‘AnnotationHub’
.taxIdToOrgDbName: no visible global function definition for
  ‘AnnotationHub’
available.GTFsForTxDbs: no visible global function definition for
  ‘AnnotationHub’
makeHubGTFIntoTxDb: no visible global function definition for
  ‘makeTxDbFromGRanges’
makeOrganismDbFromBiomart: no visible binding for global variable
  ‘DEFAULT_CIRC_SEQS’
makeOrganismDbFromBiomart: no visible global function definition for
  ‘makeTxDbFromBiomart’
makeOrganismDbFromTxDb: no visible global function definition for
  ‘isSingleStringOrNA’
makeOrganismDbFromUCSC: no visible binding for global variable
  ‘DEFAULT_CIRC_SEQS’
makeOrganismDbFromUCSC: no visible global function definition for
  ‘makeTxDbFromUCSC’
makeOuterMcolFromInnerMcol: no visible global function definition for
  ‘elementLengths’
* 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 ... WARNING
'library' or 'require' calls not declared from:
  ‘biomaRt’ ‘rtracklayer’
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/158s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
makeOrganismDbFromBiomart 14.405  0.188  51.277
rangeBasedAccessors        8.788  0.024   8.831
OrganismDb                 7.504  0.043   7.621
makeOrganismDbFromUCSC     5.899  0.032  41.359
makeOrganismDbFromTxDb     5.843  0.076  40.916
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘OrganismDbi_unit_tests.R’ [227s/231s]
 [227s/232s] 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-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
OrganismDb7.5040.0437.621
coordinate-mapping-method0.9450.0160.962
makeOrganismDbFromBiomart14.405 0.18851.277
makeOrganismDbFromTxDb 5.843 0.07640.916
makeOrganismDbFromUCSC 5.899 0.03241.359
makeOrganismPackage0.0000.0040.001
rangeBasedAccessors8.7880.0248.831