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BioC 3.2: CHECK report for siggenes on oaxaca

This page was generated on 2016-04-23 10:22:42 -0700 (Sat, 23 Apr 2016).

Package 972/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
siggenes 1.44.0
Holger Schwender
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/siggenes
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: siggenes
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings siggenes_1.44.0.tar.gz
StartedAt: 2016-04-23 04:27:53 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:29:36 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 102.6 seconds
RetCode: 0
Status:  OK 
CheckDir: siggenes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings siggenes_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/siggenes.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘siggenes/DESCRIPTION’ ... OK
* this is package ‘siggenes’ version ‘1.44.0’
* 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 ‘siggenes’ can be installed ... [8s/8s] OK
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘KernSmooth’ ‘affy’ ‘annotate’ ‘scrime’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘annotate:::getTDRows’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("get_stat_num_denum", ..., PACKAGE = "multtest")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
checkDBs: no visible global function definition for ‘getAnnMap’
chisqEbamMissing: no visible global function definition for
  ‘rowChisq2Class’
chisqEbamMissing: no visible global function definition for
  ‘rowChisqMultiClass’
chisqStatMissing: no visible global function definition for
  ‘rowChisq2Class’
chisqStatMissing: no visible global function definition for
  ‘rowChisqMultiClass’
fuzzy.ebam: no visible global function definition for ‘rowTrendFuzzy’
fuzzy.ebam: no visible global function definition for ‘abf’
fuzzy.stat: no visible global function definition for ‘rowTrendFuzzy’
fuzzy.stat: no visible global function definition for ‘abf’
make.tablecode: no visible global function definition for
  ‘cleancdfname’
make.tablecode: no visible global function definition for ‘geneNames’
make.tablecode: no visible global function definition for ‘lookUp’
make.tablecode: no visible global function definition for
  ‘shortenGeneDescription’
nclass.wand: no visible global function definition for ‘dpih’
trend.ebam.list: no visible global function definition for ‘rowCATTs’
trend.ebam.list: no visible global function definition for
  ‘rowMsquares’
trend.stat.list: no visible global function definition for ‘rowCATTs’
trend.stat.list: no visible global function definition for
  ‘rowMsquares’
identify,SAM : .local: no visible global function definition for
  ‘lookUp’
identify,SAM : .local: no visible global function definition for
  ‘getSYMBOL’
summary,EBAM : .local: no visible global function definition for
  ‘lookUp’
summary,EBAM : .local: no visible global function definition for
  ‘getSYMBOL’
summary,SAM : .local: no visible global function definition for
  ‘lookUp’
summary,SAM : .local: no visible global function definition for
  ‘getSYMBOL’
* 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 ... [3s/3s] 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-3.2-bioc/meat/siggenes.Rcheck/00check.log’
for details.


siggenes.Rcheck/00install.out:

* installing *source* package ‘siggenes’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘siggenes’
Creating a generic function for ‘identify’ from package ‘graphics’ in package ‘siggenes’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (siggenes)

siggenes.Rcheck/siggenes-Ex.timings:

nameusersystemelapsed
EBAM-class0.0020.0000.002
SAM-class0.0020.0000.002
chisq.ebam0.0010.0000.001
chisq.stat0.0020.0000.002
delta.plot0.0010.0010.001
denspr0.0000.0000.001
ebam0.0020.0000.003
find.a00.0010.0000.001
help.ebam0.0010.0000.001
help.finda00.0010.0000.001
help.sam0.0010.0010.001
list.siggenes0.0010.0000.001
md.plot0.0010.0000.001
pi0.est0.0000.0010.001
qvalue.cal0.0010.0000.001
sam0.0020.0000.001
sam.plot20.0000.0000.001
trend.ebam0.0010.0000.001
trend.stat0.0020.0000.001