Package: prot2D

Version: 1.19.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:prot2D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings prot2D_1.19.1.tar.gz

StartedAt: 2018-10-29 02:59:42 -0400 (Mon, 29 Oct 2018)

EndedAt: 2018-10-29 03:00:53 -0400 (Mon, 29 Oct 2018)

EllapsedTime: 70.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: prot2D.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:prot2D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings prot2D_1.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/prot2D.Rcheck’
* using R Under development (unstable) (2018-04-05 r74542)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prot2D/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘prot2D’ version ‘1.19.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘fdrtool’ ‘st’ ‘samr’ ‘Biobase’ ‘limma’ ‘Mulcom’ ‘impute’ ‘MASS’
  ‘qvalue’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘prot2D’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'prot2D' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/prot2D.Rcheck/00install.out’ for details.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘fdrtool’ ‘limma’ ‘samr’ ‘st’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Mulcom’ ‘impute’
  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
ES.prot: no visible global function definition for ‘new’
Norm.qt: no visible global function definition for ‘normalizeQuantiles’
Norm.qt: no visible global function definition for ‘par’
Norm.vsn: no visible global function definition for ‘normalizeVSN’
Norm.vsn: no visible global function definition for ‘par’
RIplot: no visible global function definition for ‘plot’
RIplot: no visible global function definition for ‘grey’
RIplot: no visible global function definition for ‘abline’
RIplot: no visible global function definition for ‘points’
RIplot: no visible global function definition for ‘text’
Sim.Prot.2D: no visible global function definition for ‘rchisq’
Sim.Prot.2D: no visible global function definition for ‘runif’
Sim.Prot.2D: no visible global function definition for ‘rnorm’
efronT.Prot: no visible global function definition for ‘abline’
modT.Prot: no visible global function definition for ‘abline’
robust.fdr : lts.rank.regr: no visible global function definition for
  ‘ltsreg’
robust.fdr : lts.rank.regr: no visible global function definition for
  ‘approx’
robust.fdr: no visible global function definition for ‘approx’
samT.Prot: no visible global function definition for ‘abline’
shrinkT.Prot: no visible global function definition for ‘abline’
ttest.Prot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approx grey ltsreg new normalizeQuantiles normalizeVSN par
  plot points rchisq rnorm runif text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "text")
  importFrom("methods", "new")
  importFrom("stats", "approx", "rchisq", "rnorm", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘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-3.9-bioc/meat/prot2D.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL prot2D
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘prot2D’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'prot2D' is deprecated and will be removed from Bioconductor
  version 3.9
* DONE (prot2D)

name	user	system	elapsed
ES.prot	0.277	0.024	0.303
Norm.qt	0.096	0.005	0.102
Norm.vsn	0.405	0.021	0.431
RIplot	0.048	0.005	0.054
Sim.Prot.2D	1.842	0.034	1.885
prot2D-package	1.790	0.010	1.806
variousT	1.724	0.013	1.745