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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:vissE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings vissE_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/vissE.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vissE/DESCRIPTION’ ... OK
* this is package ‘vissE’ version ‘1.16.0’
* 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 ‘vissE’ 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
checkGroups: no visible global function definition for ‘na.omit’
plotGeneStats: no visible binding for global variable ‘Count’
plotGeneStats: no visible binding for global variable ‘GeneStat’
plotGeneStats: no visible binding for global variable ‘Gene’
plotMsigNetwork: no visible binding for global variable ‘Size’
plotMsigNetwork: no visible binding for global variable ‘Category’
plotMsigNetwork: no visible binding for global variable ‘x’
plotMsigNetwork: no visible binding for global variable ‘y’
plotMsigNetwork: no visible binding for global variable ‘NodeGroup’
plotMsigPPI: no visible binding for global variable ‘weight’
plotMsigPPI: no visible binding for global variable ‘Degree’
plotMsigPPI: no visible binding for global variable ‘label’
plotMsigPPI: no visible binding for global variable ‘Label’
plotMsigWordcloud: no visible binding for global variable ‘word’
plotMsigWordcloud: no visible binding for global variable ‘freq’
plotMsigWordcloud: no visible binding for global variable ‘angle’
Undefined global functions or variables:
  Category Count Degree Gene GeneStat Label NodeGroup Size angle freq
  label na.omit weight word x y
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'computeMsigWordFreq.Rd':
  ‘[GSEABase:getObjects]{GSEABase::getBroadSets()}’

Non-topic package-anchored link(s) in Rd file 'plotGeneStats.Rd':
  ‘[GSEABase:getObjects]{GSEABase::getBroadSets()}’

Non-topic package-anchored link(s) in Rd file 'plotMsigPPI.Rd':
  ‘[GSEABase:getObjects]{GSEABase::getBroadSets()}’

Non-topic package-anchored link(s) in Rd file 'plotMsigWordcloud.Rd':
  ‘[GSEABase:getObjects]{GSEABase::getBroadSets()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... NOTE
  'LazyDataCompression' is specified without 'LazyData'
* 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
plotMsigPPI         11.354  0.762  15.778
plotMsigWordcloud    9.562  2.033  18.531
computeMsigWordFreq  7.387  0.443  13.764
characteriseGeneset  5.533  0.256   5.801
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/vissE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL vissE
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘vissE’ ...
** this is package ‘vissE’ version ‘1.16.0’
** using staged installation
** R
** data
** 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 (vissE)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(vissE)
> 
> test_check("vissE")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 63 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 63 ]
> 
> proc.time()
   user  system elapsed 
 34.770   2.801  48.873