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BioC 3.4: CHECK report for les on moscato1

This page was generated on 2016-09-21 03:43:09 -0700 (Wed, 21 Sep 2016).

Package 652/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
les 1.23.0
Julian Gehring
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/les
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: les
Version: 1.23.0
Command: rm -rf les.buildbin-libdir les.Rcheck && mkdir les.buildbin-libdir les.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=les.buildbin-libdir les_1.23.0.tar.gz >les.Rcheck\00install.out 2>&1 && cp les.Rcheck\00install.out les-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=les.buildbin-libdir --install="check:les-install.out" --force-multiarch --no-vignettes --timings les_1.23.0.tar.gz
StartedAt: 2016-09-20 11:06:18 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:08:16 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 117.9 seconds
RetCode: 0
Status:  OK  
CheckDir: les.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf les.buildbin-libdir les.Rcheck && mkdir les.buildbin-libdir les.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=les.buildbin-libdir les_1.23.0.tar.gz >les.Rcheck\00install.out 2>&1 && cp les.Rcheck\00install.out les-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=les.buildbin-libdir --install="check:les-install.out" --force-multiarch --no-vignettes --timings les_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/les.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'les/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'les' version '1.23.0'
* 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 'les' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
Package in Depends field not imported from: 'fdrtool'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'stats:::lm.wfit'
  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:
  'calcSingle' 'cdfDuplicates' 'checkState' 'diagSquare' 'fitGsri'
  'gsri' 'itLinReg' 'mcsapply' 'modGrenander' 'qrSlope' 'reg2log'
  'seSlopeWeight' 'setState' 'slopeWeight' 'wcdf2' 'wcdfGrenander'
  'xvalWeight'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("C_isomean", ..., PACKAGE = "fdrtool")
Call with DUP:
   .C("C_isomean", as.double(rawslope), as.double(dx), as.integer(n), 
       ghat = double(n), PACKAGE = "fdrtool", DUP = FALSE)
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
les-package 15.31      0   15.31
ci          11.37      0   11.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
les-package 18.05   0.00   18.05
ci          13.61   0.02   13.64
chi2         5.69   0.00    5.69
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/les.Rcheck/00check.log'
for details.


les.Rcheck/00install.out:


install for i386

* installing *source* package 'les' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'les'
Creating a generic function for 'summary' from package 'base' in package 'les'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'les' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'les' as les_1.23.0.zip
* DONE (les)

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

nameusersystemelapsed
Les-class000
Les0.040.000.05
chi24.750.024.77
ci11.37 0.0011.37
estimate0.340.000.34
export000
les-package15.31 0.0015.31
plot0.340.010.36
regions0.340.000.34
threshold0.360.000.36
weighting0.020.000.01

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

nameusersystemelapsed
Les-class000
Les0.050.000.05
chi25.690.005.69
ci13.61 0.0213.64
estimate0.450.000.45
export000
les-package18.05 0.0018.05
plot0.430.000.43
regions0.450.000.45
threshold0.420.000.42
weighting000