Package: iontree

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iontree_1.24.0.tar.gz

StartedAt: 2018-04-12 05:21:33 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:22:15 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 42.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: iontree.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iontree_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/iontree.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.24.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'iontree' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/iontree.Rcheck/00install.out’ for details.
* 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
buildIonTree: no visible binding for global variable ‘median’
metaDataImport: no visible global function definition for
  ‘flush.console’
metaDataImport: no visible global function definition for ‘fix’
plotSpectrum: no visible global function definition for ‘text’
plotSpectrum: no visible global function definition for ‘identify’
saveMSnRaw: no visible global function definition for ‘flush.console’
searchMS2: no visible global function definition for ‘par’
plot,iontree: no visible global function definition for ‘par’
plot,iontree: no visible global function definition for ‘layout’
Undefined global functions or variables:
  fix flush.console identify layout median par text
Consider adding
  importFrom("graphics", "identify", "layout", "par", "text")
  importFrom("stats", "median")
  importFrom("utils", "fix", "flush.console")
to your NAMESPACE file.
* 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 ... 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/iontree.Rcheck/00check.log’
for details.

* installing *source* package ‘iontree’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'iontree' is deprecated and will be removed from Bioconductor
  version 3.7
* DONE (iontree)

name	user	system	elapsed
buildIonTree	0.000	0.000	0.001
createDB	0	0	0
formatSpec	0.001	0.000	0.001
iontree-class	0.001	0.000	0.002
metaDataImport	0.001	0.000	0.001
mzImport	0.001	0.001	0.000
saveMSnRaw	0.001	0.000	0.001
topIons	0.000	0.000	0.001