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BioC 2.13: CHECK report for les on moscato1

This page was generated on 2014-04-05 09:50:09 -0700 (Sat, 05 Apr 2014).

Package 394/750HostnameOS / ArchBUILDCHECKBUILD BIN
les 1.12.0
Julian Gehring
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/les
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: les
Version: 1.12.0
Command: rm -rf les.buildbin-libdir && mkdir les.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=les.buildbin-libdir les_1.12.0.tar.gz >les-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=les.buildbin-libdir --install="check:les-install.out" --force-multiarch --no-vignettes --timings les_1.12.0.tar.gz && mv les.buildbin-libdir/* les.Rcheck/ && rmdir les.buildbin-libdir
StartedAt: 2014-04-05 04:49:30 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:51:57 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 146.6 seconds
RetCode: 0
Status:  OK  
CheckDir: les.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/les.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.12.0'
* 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'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* 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' ... [47s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
les-package 19.83   0.00   19.83
ci          14.23   0.03   14.26
chi2         9.02   0.00    9.01
** running examples for arch 'x64' ... [56s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
les-package 24.68   0.01   24.69
ci          17.02   0.04   17.05
chi2         9.73   0.01    9.76
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-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_1.12.0.zip
* DONE (les)

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

nameusersystemelapsed
Les-class000
Les0.030.020.05
chi29.020.009.01
ci14.23 0.0314.26
estimate0.790.000.80
export000
les-package19.83 0.0019.83
plot0.540.000.55
regions0.550.020.56
threshold0.540.000.55
weighting0.040.000.03

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

nameusersystemelapsed
Les-class000
Les0.030.000.03
chi29.730.019.76
ci17.02 0.0417.05
estimate0.640.000.64
export0.020.000.02
les-package24.68 0.0124.69
plot0.650.000.66
regions0.720.000.72
threshold0.940.020.95
weighting0.020.000.02