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BioC 3.7: CHECK report for domainsignatures on merida2

This page was generated on 2017-10-27 07:05:59 -0400 (Fri, 27 Oct 2017).

Package 382/1468HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
domainsignatures 1.37.2
Florian Hahne
Snapshot Date: 2017-10-26 17:00:16 -0400 (Thu, 26 Oct 2017)
URL: https://git.bioconductor.org/packages/domainsignatures
Branch: master
Last Commit: d0d46dc
Last Changed Date: 2017-10-20 22:14:45 -0400 (Fri, 20 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: domainsignatures
Version: 1.37.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings domainsignatures_1.37.2.tar.gz
StartedAt: 2017-10-26 22:35:04 -0400 (Thu, 26 Oct 2017)
EndedAt: 2017-10-26 22:36:55 -0400 (Thu, 26 Oct 2017)
EllapsedTime: 111.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: domainsignatures.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings domainsignatures_1.37.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/domainsignatures.Rcheck’
* using R Under development (unstable) (2017-10-21 r73570)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘domainsignatures/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘domainsignatures’ version ‘1.37.2’
* 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 ‘domainsignatures’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'domainsignatures' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/domainsignatures.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘prada’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KEGG.db’ ‘biomaRt’ ‘methods’ ‘prada’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compSimilarities: no visible global function definition for ‘progress’
compSimilarities: no visible global function definition for
  ‘killProgress’
compSimilarities: no visible global function definition for
  ‘updateProgress’
dataSource: no visible global function definition for ‘useMart’
dataSource: no visible global function definition for ‘getBM’
dataSource: no visible global function definition for ‘listLen’
dataSource: no visible global function definition for ‘new’
getKEGGdata: no visible binding for global variable ‘KEGGPATHID2EXTID’
getKEGGdata: no visible global function definition for ‘useMart’
getKEGGdata: no visible global function definition for ‘getBM’
getKEGGdata: no visible global function definition for ‘new’
getKEGGdescription: no visible binding for global variable
  ‘KEGGPATHID2NAME’
resampleGeneLists: no visible global function definition for ‘listLen’
sage.test: no visible global function definition for ‘pbinom’
sage.test: no visible global function definition for ‘chisq.test’
sage.test: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  KEGGPATHID2EXTID KEGGPATHID2NAME chisq.test dbinom getBM killProgress
  listLen new pbinom progress updateProgress useMart
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "chisq.test", "dbinom", "pbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/domainsignatures.Rcheck/00check.log’
for details.


domainsignatures.Rcheck/00install.out:

* installing *source* package ‘domainsignatures’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'domainsignatures' is deprecated and will be removed from
  Bioconductor version 3.7
* DONE (domainsignatures)

domainsignatures.Rcheck/domainsignatures-Ex.timings:

nameusersystemelapsed
dataSource0.0020.0000.002
getKEGGdata0.0010.0000.001
getKEGGdescription0.2300.0020.234
gseDomain0.0010.0000.001