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BioC 3.2: CHECK report for charm on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:04 -0400 (Tue, 27 Oct 2015).

Package 159/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
charm 2.16.0
Peter Murakami
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/charm
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: charm
Version: 2.16.0
Command: rm -rf charm.buildbin-libdir charm.Rcheck && mkdir charm.buildbin-libdir charm.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=charm.buildbin-libdir charm_2.16.0.tar.gz >charm.Rcheck\00install.out 2>&1 && cp charm.Rcheck\00install.out charm-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=charm.buildbin-libdir --install="check:charm-install.out" --force-multiarch --no-vignettes --timings charm_2.16.0.tar.gz
StartedAt: 2015-10-27 00:25:51 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 00:46:49 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 1258.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: charm.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf charm.buildbin-libdir charm.Rcheck && mkdir charm.buildbin-libdir charm.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=charm.buildbin-libdir charm_2.16.0.tar.gz >charm.Rcheck\00install.out 2>&1 && cp charm.Rcheck\00install.out charm-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=charm.buildbin-libdir --install="check:charm-install.out" --force-multiarch --no-vignettes --timings charm_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/charm.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'charm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'charm' version '2.16.0'
* 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 whether package 'charm' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages in Depends field not imported from:
  'SQN' 'fields' 'genefilter'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'oligo:::pm'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SQNff: no visible global function definition for 'Mclust'
arrayImage: no visible global function definition for
  'discretize.image'
arrayPlot: no visible global function definition for 'image.plot'
cmdsplot: no visible global function definition for 'pData'
cmdsplot: no visible global function definition for 'ffapply'
cmdsplot: no visible global function definition for 'rowSds'
controlQC: no visible global function definition for 'pData'
dmrFind: no visible global function definition for 'ffapply'
get.tt.paired: no visible global function definition for 'rowVars'
plot_CpG: no visible global function definition for 'matchPattern'
regionMatch: no visible global function definition for 'IRanges'
rowCor: no visible global function definition for 'rowSds'
spatialAdjust: no visible global function definition for
  'discretize.image'
spatialAdjustVec: no visible global function definition for
  'image.smooth'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [489s] WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
** running examples for arch 'x64' ... [500s] WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/charm.Rcheck/00check.log'
for details.

charm.Rcheck/00install.out:


install for i386

* installing *source* package 'charm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'charm' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'charm' as charm_2.16.0.zip
* DONE (charm)

charm.Rcheck/examples_i386/charm-Ex.timings:

nameusersystemelapsed
bgAdjust000
clusterMaker000
cmdsplot000
controlQC000

charm.Rcheck/examples_x64/charm-Ex.timings:

nameusersystemelapsed
bgAdjust000
clusterMaker000
cmdsplot000
controlQC000