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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gep2pep.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gep2pep_1.24.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/gep2pep.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gep2pep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gep2pep' version '1.24.0'
* 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 whether package 'gep2pep' 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) as.CategorizedCollection.Rd:27: Lost braces; missing escapes or markup?
    27 |     in the collection to {CategorizedCollection}. If
       |                          ^
checkRd: (-1) gep2pep-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:58-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:71-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loadESmatrix.Rd:19: Lost braces
    19 |     reports the ES for the pathway \code{i}, condition{j}. If
       |                                                       ^
checkRd: (-1) loadPVmatrix.Rd:19: Lost braces
    19 |     reports the PV for the pathway \code{i}, condition{j}. If
       |                                                       ^
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
createMergedRepository   0.94   6.42    9.13
PathSEA                  1.00   5.42    7.29
CondSEA                  1.01   4.11    6.03
buildPEPs                1.14   3.98    6.11
clearCache               0.88   4.08    6.30
getDetails               0.74   4.05    5.60
loadESmatrix             0.66   4.09    5.50
exportSEA                0.67   4.04    5.67
loadPVmatrix             0.62   4.03    5.47
getResults               0.61   3.98    5.43
as.CategorizedCollection 0.45   4.08    5.13
* 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 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/gep2pep.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL gep2pep
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'gep2pep' ...
** using staged installation
** R
** 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 (gep2pep)

R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(gep2pep)
> 
> test_check("gep2pep")
Chunk 1 of 2, 520 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 665 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 540 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 691 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 685 bytes (current file size: 16.3 Kb)
[ FAIL 0 | WARN 2269 | SKIP 1 | PASS 154 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_rawMode.R:216:1'

[ FAIL 0 | WARN 2269 | SKIP 1 | PASS 154 ]
> 
> proc.time()
   user  system elapsed 
  31.84   37.62   79.18