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BioC 3.0: CHECK report for ITALICS on moscato1

This page was generated on 2015-04-10 09:45:22 -0700 (Fri, 10 Apr 2015).

Package 469/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ITALICS 2.26.0
Guillem Rigaill
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ITALICS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: ITALICS
Version: 2.26.0
Command: rm -rf ITALICS.buildbin-libdir ITALICS.Rcheck && mkdir ITALICS.buildbin-libdir ITALICS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ITALICS.buildbin-libdir ITALICS_2.26.0.tar.gz >ITALICS.Rcheck\00install.out 2>&1 && cp ITALICS.Rcheck\00install.out ITALICS-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ITALICS.buildbin-libdir --install="check:ITALICS-install.out" --force-multiarch --no-vignettes --timings ITALICS_2.26.0.tar.gz
StartedAt: 2015-04-10 02:27:51 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:32:10 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 258.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ITALICS.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ITALICS.buildbin-libdir ITALICS.Rcheck && mkdir ITALICS.buildbin-libdir ITALICS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ITALICS.buildbin-libdir ITALICS_2.26.0.tar.gz >ITALICS.Rcheck\00install.out 2>&1 && cp ITALICS.Rcheck\00install.out ITALICS-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ITALICS.buildbin-libdir --install="check:ITALICS-install.out" --force-multiarch --no-vignettes --timings ITALICS_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ITALICS.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ITALICS/DESCRIPTION' ... OK
* this is package 'ITALICS' version '2.26.0'
* 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 'ITALICS' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'pd.mapping50k.xba240' was built under R version 3.2.0
See 'D:/biocbld/bbs-3.0-bioc/meat/ITALICS.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'affxparser' 'GLAD' 'oligo'
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
** 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
Packages in Depends field not imported from:
  'ITALICSData' 'pd.mapping50k.xba240'
  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
trainITALICS: warning in list.files(dir, full.name = TRUE): partial
  argument match of 'full.name' to 'full.names'
* checking Rd files ... NOTE
prepare_Rd: GLAD.GLAD.Rd:33: Dropping empty section \keyword
prepare_Rd: ITALICSNew.Rd:82: Dropping empty section \keyword
prepare_Rd: ITALICSTrain.Rd:43: Dropping empty section \keyword
prepare_Rd: Model.GetConfDat.Rd:23: Dropping empty section \keyword
prepare_Rd: Model.GetCorrection.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetEffet.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetModel.Rd:21: Dropping empty section \keyword
prepare_Rd: Model.GetResidu.Rd:18: Dropping empty section \keyword
prepare_Rd: New.AddInfo.Rd:24: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:31: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:25: Dropping empty section \examples
prepare_Rd: New.fromSnpToQuartet.Rd:25: Dropping empty section \keyword
prepare_Rd: New.getQuartet.Rd:27: Dropping empty section \keyword
prepare_Rd: New.getSnpInfo.Rd:25: Dropping empty section \keyword
prepare_Rd: New.readQuartetCopyNb.Rd:23: Dropping empty section \keyword
* 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' ... [8s] OK
** running examples for arch 'x64' ... [11s] 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/ITALICS.Rcheck/00check.log'
for details.

ITALICS.Rcheck/00install.out:


install for i386

* installing *source* package 'ITALICS' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'pd.mapping50k.xba240' was built under R version 3.2.0
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'pd.mapping50k.xba240' was built under R version 3.2.0

install for x64

* installing *source* package 'ITALICS' ...
** testing if installed package can be loaded
Warning: package 'pd.mapping50k.xba240' was built under R version 3.2.0
* MD5 sums
packaged installation of 'ITALICS' as ITALICS_2.26.0.zip
* DONE (ITALICS)

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

nameusersystemelapsed
ITALICSNew000

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

nameusersystemelapsed
ITALICSNew000