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BioC 3.2: CHECK report for HELP on moscato1

This page was generated on 2016-04-23 10:16:39 -0700 (Sat, 23 Apr 2016).

Package 488/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HELP 1.28.0
Reid F. Thompson
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/HELP
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HELP
Version: 1.28.0
Command: rm -rf HELP.buildbin-libdir HELP.Rcheck && mkdir HELP.buildbin-libdir HELP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HELP.buildbin-libdir HELP_1.28.0.tar.gz >HELP.Rcheck\00install.out 2>&1 && cp HELP.Rcheck\00install.out HELP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=HELP.buildbin-libdir --install="check:HELP-install.out" --force-multiarch --no-vignettes --timings HELP_1.28.0.tar.gz
StartedAt: 2016-04-23 03:34:50 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:36:13 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 82.1 seconds
RetCode: 0
Status:  OK  
CheckDir: HELP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HELP.buildbin-libdir HELP.Rcheck && mkdir HELP.buildbin-libdir HELP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HELP.buildbin-libdir HELP_1.28.0.tar.gz >HELP.Rcheck\00install.out 2>&1 && cp HELP.Rcheck\00install.out HELP-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=HELP.buildbin-libdir --install="check:HELP-install.out" --force-multiarch --no-vignettes --timings HELP_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/HELP.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HELP/DESCRIPTION' ... OK
* this is package 'HELP' version '1.28.0'
* 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 'HELP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcTm,character : .local: no visible binding for global variable
  'base.stacking.thermodynamics'
* 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' ... [3s] OK
** running examples for arch 'x64' ... [3s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/HELP.Rcheck/00check.log'
for details.


HELP.Rcheck/00install.out:


install for i386

* installing *source* package 'HELP' ...
** R
** data
** demo
** 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 'HELP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HELP' as HELP_1.28.0.zip
* DONE (HELP)

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

nameusersystemelapsed
base.stacking.thermodynamics0.010.000.01
calcGC000
calcPrototype0.030.000.03
calcTm0.000.020.02
combineData000
createWiggle000
exprs2000
fuzzyMatches000
getFeatures0.080.010.10
getSamples0.030.000.03
plotBins0.080.000.07
plotChip0.250.000.25
plotFeature0.110.000.11
plotPairs0.730.000.74
quantileNormalize0.070.000.12
readDesign0.090.000.31
readPairs0.110.000.11
readSampleKey000

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

nameusersystemelapsed
base.stacking.thermodynamics0.030.000.03
calcGC000
calcPrototype0.070.000.08
calcTm0.020.000.01
combineData0.020.000.02
createWiggle0.010.000.01
exprs2000
fuzzyMatches000
getFeatures0.100.020.11
getSamples0.040.000.05
plotBins0.20.00.2
plotChip0.220.000.22
plotFeature0.130.000.13
plotPairs0.720.000.71
quantileNormalize0.060.000.07
readDesign0.140.010.17
readPairs0.110.000.11
readSampleKey0.010.000.01