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BioC 3.0: CHECK report for PAnnBuilder on perceval

This page was generated on 2015-04-10 09:54:24 -0700 (Fri, 10 Apr 2015).

Package 636/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAnnBuilder 1.30.1
Li Hong
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/PAnnBuilder
Last Changed Rev: 96613 / Revision: 102249
Last Changed Date: 2014-11-07 13:38:49 -0800 (Fri, 07 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: PAnnBuilder
Version: 1.30.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PAnnBuilder_1.30.1.tar.gz
StartedAt: 2015-04-10 04:36:37 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:39:19 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 162.0 seconds
RetCode: 0
Status:  OK 
CheckDir: PAnnBuilder.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PAnnBuilder_1.30.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/PAnnBuilder.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAnnBuilder/DESCRIPTION’ ... OK
* this is package ‘PAnnBuilder’ version ‘1.30.1’
* 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 ‘PAnnBuilder’ can be installed ... [15s/18s] 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:
  ‘methods’ ‘utils’ ‘Biobase’ ‘RSQLite’ ‘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
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
':::' calls which should be '::':
  ‘AnnotationDbi:::as.list’ ‘base:::get’ ‘tools:::list_files_with_type’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::createAnnDbBimaps’
  ‘AnnotationDbi:::prefixAnnObjNames’ ‘tools:::makeLazyLoadDB’
  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:
  ‘getShortSciName’ ‘twoStepSplit’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘PAnnBuilder/R/zzz.R’:
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/PAnnBuilder.Rcheck/00check.log’
for details.

PAnnBuilder.Rcheck/00install.out:

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

PAnnBuilder.Rcheck/PAnnBuilder-Ex.timings:

nameusersystemelapsed
GOABuilder_DB0.0010.0000.002
HomoloGeneBuilder_DB0.0010.0000.001
InParanoidBuilder_DB0.0020.0010.002
PeptideAtlasBuilder_DB0.0020.0000.002
bfBuilder_DB0.0020.0000.001
crossBuilder_DB0.0020.0000.002
dNameBuilder_DB0.0010.0010.002
getSrcUrl0.0010.0000.002
intBuilder_DB0.0040.0010.005
loadFromUrl0.0010.0000.000
pBaseBuilder_DB0.0040.0000.005
pSeqBuilder_DB0.0130.0020.014
ptmBuilder_DB0.0010.0000.002
scopBuilder_DB0.0010.0000.002
subcellBuilder_DB0.0020.0000.002