Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:32 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for PLPE on machv2


To the developers/maintainers of the PLPE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PLPE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1432/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PLPE 1.54.0  (landing page)
Soo-heang Eo
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/PLPE
git_branch: RELEASE_3_14
git_last_commit: c78aa94
git_last_commit_date: 2021-10-26 11:52:51 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PLPE
Version: 1.54.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PLPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PLPE_1.54.0.tar.gz
StartedAt: 2022-04-12 16:50:11 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:50:58 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 46.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PLPE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PLPE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PLPE_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PLPE.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PLPE/DESCRIPTION’ ... OK
* this is package ‘PLPE’ version ‘1.54.0’
* 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 LazyData ... 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-3.14-bioc/meat/PLPE.Rcheck/00check.log’
for details.



Installation output

PLPE.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PLPE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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.paired0.0980.0150.112
lpe.paired.default0.0570.0090.065
lpe.paired.fdr0.2630.0160.280
lpe.paired.fdr.default0.2970.0070.304
print.lpe.paired0.0600.0080.067
summary.lpe.paired0.0530.0040.056