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CHECK report for ExpressionView on celaya2

This page was generated on 2019-10-16 12:48:02 -0400 (Wed, 16 Oct 2019).

Package 532/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ExpressionView 1.36.0
Gabor Csardi
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ExpressionView
Branch: RELEASE_3_9
Last Commit: dde1873
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ExpressionView
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExpressionView.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExpressionView_1.36.0.tar.gz
StartedAt: 2019-10-16 02:43:48 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:47:28 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 219.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ExpressionView.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExpressionView.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExpressionView_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ExpressionView.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExpressionView/DESCRIPTION’ ... OK
* this is package ‘ExpressionView’ version ‘1.36.0’
* 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 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
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ExpressionView/libs/ExpressionView.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
ExportEV 11.349  1.937  13.339
OrderEV   4.720  1.128   5.849
* 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-3.9-bioc/meat/ExpressionView.Rcheck/00check.log’
for details.



Installation output

ExpressionView.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ExpressionView
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ExpressionView’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c order.cpp -o order.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c orderclusters.cpp -o orderclusters.o
clang++ -std=gnu++11 -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-ExpressionView/00new/ExpressionView/libs
** R
** inst
** byte-compile and prepare 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ExpressionView)

Tests output


Example timings

ExpressionView.Rcheck/ExpressionView-Ex.timings

nameusersystemelapsed
ExportEV11.349 1.93713.339
LaunchEV0.0000.0010.000
OrderEV4.7201.1285.849