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CHECK report for PAnnBuilder on malbec1

This page was generated on 2017-11-30 14:25:46 -0500 (Thu, 30 Nov 2017).

Package 996/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAnnBuilder 1.42.0
Li Hong
Snapshot Date: 2017-11-29 17:00:03 -0500 (Wed, 29 Nov 2017)
URL: https://git.bioconductor.org/packages/PAnnBuilder
Branch: RELEASE_3_6
Last Commit: 8bee67b
Last Changed Date: 2017-10-30 12:39:25 -0500 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PAnnBuilder
Version: 1.42.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PAnnBuilder_1.42.0.tar.gz
StartedAt: 2017-11-30 02:46:35 -0500 (Thu, 30 Nov 2017)
EndedAt: 2017-11-30 02:48:07 -0500 (Thu, 30 Nov 2017)
EllapsedTime: 91.6 seconds
RetCode: 0
Status:  OK 
CheckDir: PAnnBuilder.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PAnnBuilder_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PAnnBuilder.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAnnBuilder/DESCRIPTION’ ... OK
* this is package ‘PAnnBuilder’ version ‘1.42.0’
* 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 ‘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
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/PAnnBuilder.Rcheck/00check.log’
for details.



Installation output

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)

Tests output


Example timings

PAnnBuilder.Rcheck/PAnnBuilder-Ex.timings

nameusersystemelapsed
GOABuilder_DB0.0040.0000.002
HomoloGeneBuilder_DB0.0000.0000.005
InParanoidBuilder_DB0.0000.0000.001
PeptideAtlasBuilder_DB0.0000.0000.005
bfBuilder_DB0.0000.0000.001
crossBuilder_DB0.0040.0000.001
dNameBuilder_DB0.0000.0000.001
getSrcUrl0.0000.0000.005
intBuilder_DB0.0040.0000.007
loadFromUrl0.0000.0000.001
pBaseBuilder_DB0.0000.0040.007
pSeqBuilder_DB0.0480.0000.067
ptmBuilder_DB0.0040.0000.002
scopBuilder_DB0.0000.0000.001
subcellBuilder_DB0.0000.0000.002