BioC 3.1: CHECK report for ExpressionView on zin2

Package: ExpressionView

Version: 1.20.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ExpressionView_1.20.0.tar.gz

StartedAt: 2015-10-09 01:00:49 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:03:18 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 149.0 seconds

RetCode: 0

Status:  OK

CheckDir: ExpressionView.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ExpressionView_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ExpressionView.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExpressionView/DESCRIPTION’ ... OK
* this is package ‘ExpressionView’ version ‘1.20.0’
* 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 ... [14s/15s] 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’
ExportEV,Biclust: no visible global function definition for
  ‘annotation’
ExportEV,ISAModules : .local: no visible global function definition for
  ‘annotation’
ExportEV,ISAModules : .local: no visible global function definition for
  ‘featureNames’
ExportEV,ISAModules : .local: no visible global function definition for
  ‘sampleNames’
ExportEV,ISAModules : .local: no visible global function definition for
  ‘phenoData’
ExportEV,ISAModules : .local: no visible global function definition for
  ‘base64encode’
ExportEV,list: no visible global function definition for ‘base64encode’
* 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 ... [20s/24s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
ExportEV 10.285   0.07  12.661
* 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/ExpressionView.Rcheck/00check.log’
for details.

* installing *source* package ‘ExpressionView’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c order.cpp -o order.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c orderclusters.cpp -o orderclusters.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o ExpressionView.so order.o orderclusters.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/ExpressionView.Rcheck/ExpressionView/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ExpressionView)

name	user	system	elapsed
ExportEV	10.285	0.070	12.661
LaunchEV	0	0	0
OrderEV	4.007	0.008	4.802