OrganismDbi 1.8.1
Biocore Data Team
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/OrganismDbi | | Last Changed Rev: 100436 / Revision: 102249 | | Last Changed Date: 2015-03-09 14:19:10 -0700 (Mon, 09 Mar 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch OrganismDbi_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/OrganismDbi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.8.1’
* 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 ‘OrganismDbi’ can be installed ... [24s/25s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘AnnotationDbi’
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
* 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.
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::.resort’ ‘AnnotationDbi:::.testForValidKeytype’
‘AnnotationDbi:::.testSelectArgs’ ‘AnnotationDbi:::dbConn’
‘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<-’
.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<-’
.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<-’
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 ... WARNING
Missing link or links in documentation object 'OrganismDb.Rd':
‘[GenomicRanges]{seqlevels}’ ‘[GenomicRanges]{seqlengths}’
‘[GenomicRanges]{isCircular}’ ‘[GenomicRanges]{genome}’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/30s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
rangeBasedAccessors 14.099 0.643 15.991
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘OrganismDbi_unit_tests.R’ [195s/204s]
[196s/204s] 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
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.