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This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1058/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LedPred 1.34.0  (landing page)
Aitor Gonzalez
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/LedPred
git_branch: RELEASE_3_17
git_last_commit: f6749ce
git_last_commit_date: 2023-04-25 10:40:38 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for LedPred on kjohnson2


To the developers/maintainers of the LedPred package:
- 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: LedPred
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LedPred.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LedPred_1.34.0.tar.gz
StartedAt: 2023-10-18 03:38:23 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 03:40:04 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 100.8 seconds
RetCode: 0
Status:   OK  
CheckDir: LedPred.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LedPred.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LedPred_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/LedPred.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LedPred/DESCRIPTION’ ... OK
* this is package ‘LedPred’ version ‘1.34.0’
* 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 ‘LedPred’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Hotfix: Fixed sign of prediction
  Cannot process chunk/lines:
    Fixed tests
  Cannot process chunk/lines:
    Large rewritten of core architecture using object-oriented R6 classes. There are almost not changes at the user-level
  Cannot process chunk/lines:
    July 20, 2015
    ## Release Notes
    - Some bug fixes
    ## Bug fixes
    - One shot LedPred did not save model
* 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 ... NOTE
.plotCostGamma: no visible global function definition for ‘title’
.plotCostGamma: no visible global function definition for ‘points’
mapFeaturesToCRMs: no visible global function definition for
  ‘write.table’
mapFeaturesToCRMs: no visible global function definition for
  ‘read.table’
mapFeaturesToCRMs: no visible global function definition for
  ‘download.file’
scoreData: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  download.file points read.table title write.table
Consider adding
  importFrom("graphics", "points", "title")
  importFrom("utils", "download.file", "read.table", "write.table")
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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/LedPred.Rcheck/00check.log’
for details.



Installation output

LedPred.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘LedPred’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 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 (LedPred)

Tests output

LedPred.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(LedPred)
Loading required package: e1071
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
> 
> test_check("LedPred")
2023-10-18 03:39:38.026 R[99769:43258341] XType: com.apple.fonts is not accessible.
2023-10-18 03:39:38.034 R[99769:43258341] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 45 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 45 ]
> 
> proc.time()
   user  system elapsed 
 12.859   5.601  16.446 

Example timings

LedPred.Rcheck/LedPred-Ex.timings

nameusersystemelapsed
LedPred0.0600.0050.092
createModel0.0020.0020.004
evaluateModelPerformance0.0020.0020.006
mapFeaturesToCRMs000
mcTune0.0000.0010.002
rankFeatures0.0010.0010.002
scoreData0.0030.0030.009
tuneFeatureNb0.0010.0020.003