Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-07 11:09:27 -0500 (Wed, 07 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4423
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 idpr on merida1


To the developers/maintainers of the idpr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/idpr.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 939/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
idpr 1.9.0  (landing page)
William M. McFadden
Snapshot Date: 2022-12-06 14:00:17 -0500 (Tue, 06 Dec 2022)
git_url: https://git.bioconductor.org/packages/idpr
git_branch: master
git_last_commit: d4dea0b
git_last_commit_date: 2022-11-01 11:22:40 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: idpr
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:idpr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings idpr_1.9.0.tar.gz
StartedAt: 2022-12-07 02:26:19 -0500 (Wed, 07 Dec 2022)
EndedAt: 2022-12-07 02:28:19 -0500 (Wed, 07 Dec 2022)
EllapsedTime: 120.1 seconds
RetCode: 0
Status:   OK  
CheckDir: idpr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:idpr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings idpr_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/idpr.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘idpr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘idpr’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
 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 ‘idpr’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
  Note: found 13 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
sequenceMap            5.291  0.047   7.052
chargeHydropathyPlot   3.985  0.019   5.315
structuralTendencyPlot 3.822  0.032   5.165
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/idpr.Rcheck/00check.log’
for details.



Installation output

idpr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL idpr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘idpr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (idpr)

Tests output

idpr.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(idpr)
> 
> test_check("idpr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
  2.956   0.187   4.044 

Example timings

idpr.Rcheck/idpr-Ex.timings

nameusersystemelapsed
chargeCalculationGlobal1.6880.0232.258
chargeCalculationLocal0.7880.0061.037
chargeHydropathyPlot3.9850.0195.315
hendersonHasselbalch0.0550.0020.082
idprofile0.0000.0000.006
iupred0.0010.0010.001
meanScaledHydropathy0.0020.0000.003
netCharge0.1350.0010.197
scaledHydropathyGlobal0.7090.0040.980
scaledHydropathyLocal0.7400.0051.008
sequenceCheck000
sequenceMap5.2910.0477.052
sequenceMapCoordinates0.5060.0060.726
sequencePlot0.7960.0051.084
structuralTendency0.0100.0000.014
structuralTendencyPlot3.8220.0325.165