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CHECK report for PLPE on celaya2

This page was generated on 2020-01-16 13:31:30 -0500 (Thu, 16 Jan 2020).

Package 1274/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PLPE 1.47.0
Soo-heang Eo
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/PLPE
Branch: master
Last Commit: a1f3cc5
Last Changed Date: 2019-12-23 18:14:37 -0500 (Mon, 23 Dec 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PLPE
Version: 1.47.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PLPE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PLPE_1.47.0.tar.gz
StartedAt: 2020-01-16 07:31:25 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 07:32:20 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 54.2 seconds
RetCode: 0
Status:  OK 
CheckDir: PLPE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PLPE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PLPE_1.47.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PLPE.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PLPE/DESCRIPTION’ ... OK
* this is package ‘PLPE’ version ‘1.47.0’
* 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 ‘PLPE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  ‘Biobase’ ‘LPE’ ‘MASS’ ‘methods’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘LPE’
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  lpe.paired.fdr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘PLPE/R/lpe.paired.R’:
  .First.lib calls:
    cat("LPEP version 1.0.0 \n")
    require(Biobase)
    require(methods)

Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

base.error.paired: no visible global function definition for ‘na.omit’
base.error.paired: no visible global function definition for ‘quantile’
base.error.paired: no visible global function definition for ‘var’
base.error.paired: no visible global function definition for ‘median’
base.error.paired: no visible global function definition for
  ‘smooth.spline’
base.error.paired: no visible global function definition for
  ‘fixbounds.predict.smooth.spline’
generate.null: no visible global function definition for ‘quantile’
generate.null: no visible global function definition for ‘median’
lpe.paired.default: no visible binding for global variable ‘median’
lpe.paired.default: no visible binding for global variable ‘var’
lpe.paired.default: no visible binding for global variable ‘t.test’
lpe.paired.default: no visible global function definition for ‘pnorm’
lpe.paired.default: no visible global function definition for ‘lm’
lpe.paired.fdr.default: no visible global function definition for
  ‘quantile’
summary.lpe.paired: no visible global function definition for ‘head’
summary.lpe.paired.fdr: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  fixbounds.predict.smooth.spline head lm median na.omit pnorm quantile
  smooth.spline t.test var
Consider adding
  importFrom("stats", "lm", "median", "na.omit", "pnorm", "quantile",
             "smooth.spline", "t.test", "var")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'lpe.paired.fdr':
  ‘lpe.paired.fdr’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/PLPE.Rcheck/00check.log’
for details.



Installation output

PLPE.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PLPE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘PLPE’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PLPE)

Tests output


Example timings

PLPE.Rcheck/PLPE-Ex.timings

nameusersystemelapsed
lpe.paired0.0880.0250.113
lpe.paired.default0.0520.0130.066
lpe.paired.fdr0.3050.0220.327
lpe.paired.fdr.default0.3210.0130.335
print.lpe.paired0.0710.0110.082
summary.lpe.paired0.0560.0040.060