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BioC 3.1: CHECK report for OrganismDbi on moscato2

This page was generated on 2015-10-09 09:29:55 -0700 (Fri, 09 Oct 2015).

Package 684/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OrganismDbi 1.10.0
Biocore Data Team
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/OrganismDbi
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.10.0
Command: rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.10.0.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.10.0.tar.gz
StartedAt: 2015-10-09 04:33:44 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:52:30 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 1126.3 seconds
RetCode: 0
Status:  OK  
CheckDir: OrganismDbi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && mkdir OrganismDbi.buildbin-libdir OrganismDbi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OrganismDbi.buildbin-libdir OrganismDbi_1.10.0.tar.gz >OrganismDbi.Rcheck\00install.out 2>&1 && cp OrganismDbi.Rcheck\00install.out OrganismDbi-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=OrganismDbi.buildbin-libdir --install="check:OrganismDbi-install.out" --force-multiarch --no-vignettes --timings OrganismDbi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/OrganismDbi.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OrganismDbi/DESCRIPTION' ... OK
* this is package 'OrganismDbi' version '1.10.0'
* 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 whether package 'OrganismDbi' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'AnnotationDbi' 'GenomicFeatures'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'AnnotationDbi:::dbconn'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'AnnotationDbi:::.resort' 'AnnotationDbi:::.testForValidKeytype'
  'AnnotationDbi:::.testSelectArgs' 'BiocGenerics:::testPackage'
  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
.cds: no visible global function definition for 'mcols'
.cds: no visible global function definition for 'mcols<-'
.cdsBy: no visible global function definition for 'mcols'
.cdsBy: no visible global function definition for 'mcols<-'
.cdsBy: no visible global function definition for 'id2name'
.combineMetadata: no visible global function definition for 'mcols'
.compressMetadata: no visible binding for global variable 'splitAsList'
.exons: no visible global function definition for 'mcols'
.exons: no visible global function definition for 'mcols<-'
.exonsBy: no visible global function definition for 'mcols'
.exonsBy: no visible global function definition for 'mcols<-'
.exonsBy: no visible global function definition for 'id2name'
.genes: no visible global function definition for 'mcols'
.genes: no visible global function definition for 'mcols<-'
.getMetaDataValue: no visible global function definition for
  'dbGetQuery'
.makekeytypeMapping: no visible global function definition for
  'unlist2'
.transcripts: no visible global function definition for 'mcols'
.transcripts: no visible global function definition for 'mcols<-'
.transcriptsBy: no visible global function definition for 'mcols'
.transcriptsBy: no visible global function definition for 'mcols<-'
.transcriptsBy: no visible global function definition for 'id2name'
makeOrganismPackage: no visible binding for global variable
  'isSingleString'
makeOrganismPackage: no visible global function definition for
  'createPackage'
* 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 ...
** running examples for arch 'i386' ... [152s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
rangeBasedAccessors       15.80   0.22  116.36
coordinate-mapping-method  2.38   0.06   26.53
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
rangeBasedAccessors 14.08   0.19   14.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'OrganismDbi_unit_tests.R' [426s]
 [427s] OK
** running tests for arch 'x64' ...
  Running 'OrganismDbi_unit_tests.R' [298s]
 [298s] 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/OrganismDbi.Rcheck/00check.log'
for details.


OrganismDbi.Rcheck/00install.out:


install for i386

* installing *source* package 'OrganismDbi' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'OrganismDbi' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'OrganismDbi' as OrganismDbi_1.10.0.zip
* DONE (OrganismDbi)

OrganismDbi.Rcheck/examples_i386/OrganismDbi-Ex.timings:

nameusersystemelapsed
OrganismDb0.640.010.76
coordinate-mapping-method 2.38 0.0626.53
makeOrganismPackage0.100.020.30
rangeBasedAccessors 15.80 0.22116.36

OrganismDbi.Rcheck/examples_x64/OrganismDbi-Ex.timings:

nameusersystemelapsed
OrganismDb1.160.032.50
coordinate-mapping-method3.340.083.62
makeOrganismPackage0.140.000.14
rangeBasedAccessors14.08 0.1914.27