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BioC 3.4: CHECK report for CNTools on morelia

This page was generated on 2016-09-21 03:50:21 -0700 (Wed, 21 Sep 2016).

Package 227/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNTools 1.29.0
J. Zhang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CNTools
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CNTools
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNTools_1.29.0.tar.gz
StartedAt: 2016-09-20 04:45:02 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:46:29 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 87.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CNTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CNTools_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CNTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNTools/DESCRIPTION’ ... OK
* this is package ‘CNTools’ version ‘1.29.0’
* 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 ‘CNTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* 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:
  ‘methods’ ‘tools’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘genefilter:::genefilter’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getCommonSegValues’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘CNTools/R/zzz.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)
    require("tools", quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

filterByMad: no visible binding for global variable ‘mad’
filterByMad: no visible global function definition for ‘quantile’
getPairCor : pair2Cor: no visible global function definition for ‘cor’
getPairDist : pair2Dist: no visible global function definition for
  ‘dist’
getPairDist: no visible global function definition for ‘as.dist’
getCor,RS: no visible global function definition for ‘cor’
getDist,RS: no visible global function definition for ‘dist’
Undefined global functions or variables:
  as.dist cor dist mad quantile
Consider adding
  importFrom("stats", "as.dist", "cor", "dist", "mad", "quantile")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/CNTools.Rcheck/00check.log’
for details.


CNTools.Rcheck/00install.out:

* installing *source* package ‘CNTools’ ...
** 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 getratios.c -o getratios.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 CNTools.so getratios.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/CNTools.Rcheck/CNTools/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘start’ in package ‘CNTools’
Creating a new generic function for ‘end’ in package ‘CNTools’
Creating a generic function for ‘genefilter’ from package ‘genefilter’ in package ‘CNTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNTools)

CNTools.Rcheck/CNTools-Ex.timings:

nameusersystemelapsed
CNSeg-class1.1750.0171.193
RS-class0.7240.0180.743