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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PIUMA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PIUMA_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PIUMA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/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 ‘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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL PIUMA
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 78 ]
> 
> proc.time()
   user  system elapsed 
 10.021   0.632  10.641