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BioC 2.14: CHECK report for PAnnBuilder on moscato2

This page was generated on 2014-10-08 08:52:50 -0700 (Wed, 08 Oct 2014).

Package 562/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAnnBuilder 1.28.0
Li Hong
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/PAnnBuilder
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 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: PAnnBuilder
Version: 1.28.0
Command: rm -rf PAnnBuilder.buildbin-libdir && mkdir PAnnBuilder.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PAnnBuilder.buildbin-libdir PAnnBuilder_1.28.0.tar.gz >PAnnBuilder-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=PAnnBuilder.buildbin-libdir --install="check:PAnnBuilder-install.out" --force-multiarch --no-vignettes --timings PAnnBuilder_1.28.0.tar.gz
StartedAt: 2014-10-08 03:38:17 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 03:40:23 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 126.1 seconds
RetCode: 0
Status:  OK  
CheckDir: PAnnBuilder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PAnnBuilder.buildbin-libdir && mkdir PAnnBuilder.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PAnnBuilder.buildbin-libdir PAnnBuilder_1.28.0.tar.gz >PAnnBuilder-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=PAnnBuilder.buildbin-libdir --install="check:PAnnBuilder-install.out" --force-multiarch --no-vignettes --timings PAnnBuilder_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/PAnnBuilder.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PAnnBuilder/DESCRIPTION' ... OK
* this is package 'PAnnBuilder' version '1.28.0'
* 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 'PAnnBuilder' 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:
  '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
* 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
'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'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [4s] 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/PAnnBuilder.Rcheck/00check.log'
for details.

PAnnBuilder.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'PAnnBuilder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PAnnBuilder' as PAnnBuilder_1.28.0.zip
* DONE (PAnnBuilder)

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

nameusersystemelapsed
GOABuilder_DB000
HomoloGeneBuilder_DB0.020.000.01
InParanoidBuilder_DB000
PeptideAtlasBuilder_DB000
bfBuilder_DB000
crossBuilder_DB000
dNameBuilder_DB000
getSrcUrl000
intBuilder_DB000
loadFromUrl000
pBaseBuilder_DB000
pSeqBuilder_DB0.020.000.01
ptmBuilder_DB000
scopBuilder_DB0.010.000.02
subcellBuilder_DB000

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

nameusersystemelapsed
GOABuilder_DB000
HomoloGeneBuilder_DB000
InParanoidBuilder_DB000
PeptideAtlasBuilder_DB0.020.000.02
bfBuilder_DB000
crossBuilder_DB000
dNameBuilder_DB000
getSrcUrl000
intBuilder_DB000
loadFromUrl000
pBaseBuilder_DB000
pSeqBuilder_DB0.020.000.02
ptmBuilder_DB000
scopBuilder_DB000
subcellBuilder_DB000