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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1559/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PIUMA 1.2.0  (landing page)
Mattia Chiesa
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/PIUMA
git_branch: RELEASE_3_20
git_last_commit: 9561dbc
git_last_commit_date: 2024-10-29 11:30:09 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for PIUMA on kjohnson1

To the developers/maintainers of the PIUMA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PIUMA.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: PIUMA
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PIUMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PIUMA_1.2.0.tar.gz
StartedAt: 2024-12-21 04:53:40 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 04:57:29 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 229.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PIUMA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PIUMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PIUMA_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PIUMA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PIUMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PIUMA’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘PIUMA’ 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 code 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
makeTDAobjFromSE: no visible global function definition for ‘colData’
makeTDAobjFromSE: no visible global function definition for ‘assay’
plot_ScaleFreeLaw: no visible binding for global variable ‘k’
plot_ScaleFreeLaw: no visible binding for global variable ‘pk’
plot_ScaleFreeLaw: no visible global function definition for
  ‘stat_smooth’
plot_ScaleFreeLaw: no visible global function definition for
  ‘scale_x_continuous’
plot_ScaleFreeLaw: no visible binding for global variable ‘.x’
plot_projection_plot: no visible binding for global variable ‘comp1’
plot_projection_plot: no visible binding for global variable ‘comp2’
Undefined global functions or variables:
  .x assay colData comp1 comp2 k pk scale_x_continuous stat_smooth
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘jaccard’ ‘plot_ScaleFreeLaw’ ‘plot_projection_plot’ ‘scaleData_01’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 data for ASCII and uncompressed saves ... 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/PIUMA.Rcheck/00check.log’
for details.


Installation output

PIUMA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘PIUMA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘getOrigData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setOrigData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getScaledData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setScaledData’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getOutcomeFact’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setOutcomeFact’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getOutcome’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setOutcome’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getComp’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setComp’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getDistMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setDistMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getDfMapper’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setDfMapper’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getJacc’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setJacc’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘getNodeDataMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
in method for ‘setNodeDataMat’ with signature ‘x="TDAobj"’: no definition for class “TDAobj”
** 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 (PIUMA)

Tests output

PIUMA.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(PIUMA)
Loading required package: ggplot2
> 
> test_check("PIUMA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
> 
> proc.time()
   user  system elapsed 
 13.749   0.633  14.387 

Example timings

PIUMA.Rcheck/PIUMA-Ex.timings

nameusersystemelapsed
checkNetEntropy0.0010.0000.002
checkScaleFreeModel0.0040.0020.007
dfToDistance0.0050.0020.008
dfToProjection0.0070.0020.010
getComp0.0020.0020.004
getDfMapper0.0020.0020.004
getDistMat0.0020.0020.004
getJacc0.0020.0010.004
getNodeDataMat0.0020.0020.005
getOrigData0.0020.0020.004
getOutcome0.0020.0010.004
getOutcomeFact0.0020.0020.004
getScaledData0.0020.0020.005
jaccardMatrix0.0780.0120.089
makeTDAobj2.6300.0742.704
makeTDAobjFromSE1.5720.0881.659
mapperCore0.0250.0020.026
setComp0.0020.0010.004
setDfMapper0.0020.0010.003
setDistMat0.0020.0010.004
setJacc0.0020.0020.003
setNodeDataMat0.0020.0020.004
setOrigData0.0020.0020.003
setOutcome0.0020.0020.004
setOutcomeFact0.0020.0020.003
setScaledData0.0020.0010.004
tdaDfEnrichment0.0080.0030.010