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BioC 3.3: CHECK report for ITALICS on oaxaca

This page was generated on 2016-10-13 12:56:43 -0700 (Thu, 13 Oct 2016).

Package 606/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ITALICS 2.32.0
Guillem Rigaill
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ITALICS
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (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: ITALICS
Version: 2.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ITALICS_2.32.0.tar.gz
StartedAt: 2016-10-13 03:02:33 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 03:05:02 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 148.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ITALICS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ITALICS_2.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ITALICS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ITALICS/DESCRIPTION’ ... OK
* this is package ‘ITALICS’ version ‘2.32.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ITALICS’ 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.
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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/ITALICS.Rcheck/00check.log’
for details.


ITALICS.Rcheck/00install.out:

* installing *source* package ‘ITALICS’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ITALICS)

ITALICS.Rcheck/ITALICS-Ex.timings:

nameusersystemelapsed
ITALICSNew0.0010.0010.001