BioC 3.1: CHECK report for OrganismDbi on petty
This page was generated on 2015-10-09 09:35:15 -0700 (Fri, 09 Oct 2015).
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 | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: OrganismDbi |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OrganismDbi_1.10.0.tar.gz |
StartedAt: 2015-10-09 00:55:05 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 01:09:39 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 874.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OrganismDbi.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OrganismDbi_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/OrganismDbi.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OrganismDbi’ can be installed ... [26s/26s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
rangeBasedAccessors 18.601 0.901 21.541
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘OrganismDbi_unit_tests.R’ [531s/598s]
[532s/598s] 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
‘/Users/biocbuild/bbs-3.1-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.
OrganismDbi.Rcheck/00install.out:
* 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’
* DONE (OrganismDbi)
OrganismDbi.Rcheck/OrganismDbi-Ex.timings:
name | user | system | elapsed
|
OrganismDb | 1.39 | 0.07 | 1.77 |
|
coordinate-mapping-method | 3.353 | 0.122 | 3.618 |
|
makeOrganismPackage | 0.247 | 0.007 | 0.254 |
|
rangeBasedAccessors | 18.601 | 0.901 | 21.541 |
|