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BioC 3.0: CHECK report for iontree on oaxaca

This page was generated on 2015-04-10 10:05:17 -0700 (Fri, 10 Apr 2015).

Package 462/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iontree 1.12.0
Mingshu Cao
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/iontree
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  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: iontree
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iontree_1.12.0.tar.gz
StartedAt: 2015-04-10 00:40:57 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:41:53 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 55.8 seconds
RetCode: 0
Status:  OK 
CheckDir: iontree.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 --no-multiarch iontree_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/iontree.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iontree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iontree’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘iontree’ can be installed ... [4s/4s] 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createDB: no visible global function definition for ‘dbDriver’
metaDataImport: no visible global function definition for ‘dbDriver’
metaDataImport: no visible global function definition for ‘fetch’
mzImport: no visible global function definition for ‘dbDriver’
mzImport: no visible global function definition for ‘fetch’
searchMS2: no visible global function definition for ‘dbDriver’
searchMS2: no visible global function definition for ‘fetch’
* checking Rd files ... NOTE
prepare_Rd: buildIonTree.Rd:18-19: Dropping empty section \details
prepare_Rd: buildIonTree.Rd:20-26: Dropping empty section \value
prepare_Rd: buildIonTree.Rd:27-29: Dropping empty section \references
prepare_Rd: buildIonTree.Rd:37-39: Dropping empty section \seealso
prepare_Rd: createDB.Rd:19-20: Dropping empty section \details
prepare_Rd: createDB.Rd:30-32: Dropping empty section \note
prepare_Rd: createDB.Rd:24-26: Dropping empty section \references
prepare_Rd: createDB.Rd:34-36: Dropping empty section \seealso
prepare_Rd: distMS2.Rd:18-19: Dropping empty section \details
prepare_Rd: distMS2.Rd:20-22: Dropping empty section \value
prepare_Rd: distMS2.Rd:29-31: Dropping empty section \note
prepare_Rd: distMS2.Rd:32-34: Dropping empty section \seealso
prepare_Rd: distMS2.Rd:35-36: Dropping empty section \examples
prepare_Rd: formatSpec.Rd:18-19: Dropping empty section \details
prepare_Rd: formatSpec.Rd:20-22: Dropping empty section \value
prepare_Rd: formatSpec.Rd:29-31: Dropping empty section \note
prepare_Rd: formatSpec.Rd:23-25: Dropping empty section \references
prepare_Rd: formatSpec.Rd:35-37: Dropping empty section \seealso
prepare_Rd: getMSnRaw.Rd:22-23: Dropping empty section \details
prepare_Rd: getMSnRaw.Rd:29-31: Dropping empty section \references
prepare_Rd: getMSnRaw.Rd:39-41: Dropping empty section \seealso
prepare_Rd: getMSnRaw.Rd:42-43: Dropping empty section \examples
prepare_Rd: getMetaInfo.Rd:17-18: Dropping empty section \details
prepare_Rd: getMetaInfo.Rd:19-25: Dropping empty section \value
prepare_Rd: getMetaInfo.Rd:32-34: Dropping empty section \note
prepare_Rd: getMetaInfo.Rd:26-28: Dropping empty section \references
prepare_Rd: getMetaInfo.Rd:36-38: Dropping empty section \seealso
prepare_Rd: getMetaInfo.Rd:39-40: Dropping empty section \examples
prepare_Rd: hasMS2.Rd:18-19: Dropping empty section \details
prepare_Rd: hasMS2.Rd:28-29: Dropping empty section \note
prepare_Rd: hasMS2.Rd:23-24: Dropping empty section \references
prepare_Rd: hasMS2.Rd:31-32: Dropping empty section \seealso
prepare_Rd: hasMS2.Rd:33-34: Dropping empty section \examples
prepare_Rd: iontree-class.Rd:30-32: Dropping empty section \references
prepare_Rd: iontree-class.Rd:40-41: Dropping empty section \seealso
prepare_Rd: iontree-package.Rd:32-33: Dropping empty section \seealso
prepare_Rd: iontree-package.Rd:34-35: Dropping empty section \examples
prepare_Rd: metaDataImport.Rd:17-19: Dropping empty section \details
prepare_Rd: metaDataImport.Rd:20-21: Dropping empty section \value
prepare_Rd: metaDataImport.Rd:22-24: Dropping empty section \references
prepare_Rd: metaDataImport.Rd:32-34: Dropping empty section \seealso
prepare_Rd: mzImport.Rd:18-19: Dropping empty section \details
prepare_Rd: mzImport.Rd:20-22: Dropping empty section \value
prepare_Rd: mzImport.Rd:23-25: Dropping empty section \references
prepare_Rd: mzImport.Rd:33-35: Dropping empty section \seealso
prepare_Rd: plotSpectrum.Rd:29-31: Dropping empty section \details
prepare_Rd: plotSpectrum.Rd:32-38: Dropping empty section \value
prepare_Rd: plotSpectrum.Rd:45-46: Dropping empty section \note
prepare_Rd: plotSpectrum.Rd:39-41: Dropping empty section \references
prepare_Rd: plotSpectrum.Rd:48-50: Dropping empty section \seealso
prepare_Rd: plotSpectrum.Rd:51-52: Dropping empty section \examples
prepare_Rd: rs2iontree.Rd:16-17: Dropping empty section \details
prepare_Rd: rs2iontree.Rd:27-28: Dropping empty section \note
prepare_Rd: rs2iontree.Rd:21-23: Dropping empty section \references
prepare_Rd: rs2iontree.Rd:30-31: Dropping empty section \seealso
prepare_Rd: rs2iontree.Rd:33-34: Dropping empty section \examples
prepare_Rd: saveMSnRaw.Rd:17-19: Dropping empty section \details
prepare_Rd: saveMSnRaw.Rd:20-26: Dropping empty section \value
prepare_Rd: saveMSnRaw.Rd:33-35: Dropping empty section \note
prepare_Rd: saveMSnRaw.Rd:27-29: Dropping empty section \references
prepare_Rd: saveMSnRaw.Rd:36-38: Dropping empty section \seealso
prepare_Rd: searchMS2.Rd:23-25: Dropping empty section \details
prepare_Rd: searchMS2.Rd:35-36: Dropping empty section \note
prepare_Rd: searchMS2.Rd:29-31: Dropping empty section \references
prepare_Rd: searchMS2.Rd:38-40: Dropping empty section \seealso
prepare_Rd: searchMS2.Rd:41-42: Dropping empty section \examples
prepare_Rd: topIons.Rd:17-19: Dropping empty section \details
prepare_Rd: topIons.Rd:29-31: Dropping empty section \note
prepare_Rd: topIons.Rd:23-25: Dropping empty section \references
* 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 ... [2s/4s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/iontree.Rcheck/00check.log’
for details.

iontree.Rcheck/00install.out:

* installing *source* package ‘iontree’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘iontree’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iontree)

iontree.Rcheck/iontree-Ex.timings:

nameusersystemelapsed
buildIonTree0.0010.0000.001
createDB0.0000.0000.001
formatSpec0.0010.0010.001
iontree-class0.0020.0000.687
metaDataImport0.0010.0010.001
mzImport0.0000.0000.001
saveMSnRaw0.0000.0000.001
topIons0.0000.0000.001