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This page was generated on 2024-03-27 11:37:00 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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

Package 1564/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PLPE 1.62.0  (landing page)
Soo-heang Eo
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/PLPE
git_branch: RELEASE_3_18
git_last_commit: 19a299c
git_last_commit_date: 2023-10-24 09:40:30 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for PLPE on palomino4


To the developers/maintainers of the PLPE package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: PLPE
Version: 1.62.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PLPE.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings PLPE_1.62.0.tar.gz
StartedAt: 2024-03-26 03:53:18 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 03:53:56 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 37.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PLPE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PLPE.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings PLPE_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/PLPE.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PLPE/DESCRIPTION' ... OK
* this is package 'PLPE' version '1.62.0'
* 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 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 ... OK
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/PLPE.Rcheck/00check.log'
for details.



Installation output

PLPE.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL PLPE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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.paired0.050.030.09
lpe.paired.default0.040.000.05
lpe.paired.fdr0.120.020.14
lpe.paired.fdr.default0.110.020.13
print.lpe.paired0.030.000.03
summary.lpe.paired0.020.000.01