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BioC 3.4: CHECK report for ExpressionView on morelia

This page was generated on 2017-03-03 16:20:01 -0500 (Fri, 03 Mar 2017).

Package 401/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ExpressionView 1.26.0
Gabor Csardi
Snapshot Date: 2017-03-02 17:15:05 -0500 (Thu, 02 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ExpressionView
Last Changed Rev: 122710 / Revision: 127118
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ExpressionView
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ExpressionView_1.26.0.tar.gz
StartedAt: 2017-03-03 02:50:37 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 02:53:19 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 162.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ExpressionView.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ExpressionView_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ExpressionView.Rcheck’
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExpressionView/DESCRIPTION’ ... OK
* this is package ‘ExpressionView’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘caTools’ ‘bitops’ ‘isa2’ ‘eisa’ ‘GO.db’ ‘KEGG.db’ ‘AnnotationDbi’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ExpressionView’ 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’ ‘isa2’ ‘eisa’ ‘GO.db’ ‘KEGG.db’ ‘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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘AnnotationDbi’ ‘GO.db’ ‘KEGG.db’
  Please remove these calls from your code.
'library' or 'require' call to ‘affy’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘isa2::.onUnload’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .Last.lib will not be used unless it is exported

ExportEV.Biclust: no visible global function definition for
  ‘annotation’
ExportEV.ISAModules: no visible global function definition for
  ‘annotation’
ExportEV.ISAModules: no visible global function definition for
  ‘featureNames’
ExportEV.ISAModules: no visible global function definition for
  ‘sampleNames’
ExportEV.ISAModules: no visible global function definition for
  ‘phenoData’
ExportEV.ISAModules: no visible global function definition for
  ‘base64encode’
ExportEV.list: no visible global function definition for ‘base64encode’
LaunchEV: no visible global function definition for ‘URLencode’
LaunchEV: no visible global function definition for ‘browseURL’
OrderEV.list: no visible global function definition for ‘flush.console’
normalize: no visible global function definition for ‘hist’
ExportEV,Biclust: no visible global function definition for
  ‘annotation’
ExportEV,ISAModules: no visible global function definition for
  ‘annotation’
ExportEV,ISAModules: no visible global function definition for
  ‘featureNames’
ExportEV,ISAModules: no visible global function definition for
  ‘sampleNames’
ExportEV,ISAModules: no visible global function definition for
  ‘phenoData’
ExportEV,ISAModules: no visible global function definition for
  ‘base64encode’
ExportEV,list: no visible global function definition for ‘base64encode’
OrderEV,list: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  URLencode annotation base64encode browseURL featureNames
  flush.console hist phenoData sampleNames
Consider adding
  importFrom("graphics", "hist")
  importFrom("utils", "URLencode", "browseURL", "flush.console")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘ExpressionView/libs/ExpressionView.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘orderclusters.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
ExportEV 9.846  0.654  10.537
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/ExpressionView.Rcheck/00check.log’
for details.


ExpressionView.Rcheck/00install.out:

* installing *source* package ‘ExpressionView’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c order.cpp -o order.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c orderclusters.cpp -o orderclusters.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ExpressionView.so order.o orderclusters.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/ExpressionView.Rcheck/ExpressionView/libs
** R
** inst
** preparing package for lazy loading
in method for ‘ExportEV’ with signature ‘biclusters="Biclust"’: no definition for class “Biclust”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ExpressionView)

ExpressionView.Rcheck/ExpressionView-Ex.timings:

nameusersystemelapsed
ExportEV 9.846 0.65410.537
LaunchEV0.0010.0000.000
OrderEV3.6310.4244.056