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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RcisTarget_1.28.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RcisTarget.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RcisTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RcisTarget’ version ‘1.28.1’
* 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 ‘RcisTarget’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
* 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) dbRegionsLoc.Rd:11-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbRegionsLoc.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importAnnotations.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:27-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importAnnotations.Rd:33-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) motifAnnotations.Rd:18-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:58-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) motifAnnotations.Rd:63-66: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RcisTarget.Rd: GeneSet, GeneSetCollection
  calcAUC.Rd: GeneSet, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
addMotifAnnotation      19.493  1.007  20.455
addSignificantGenes     15.212  1.180  16.380
getMotifAnnotation       8.830  0.248   9.034
aucScores-class          7.829  0.415   8.245
reRank                   7.420  0.310   7.731
rankingRcisTarget-class  6.985  0.150   7.137
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RcisTarget.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL RcisTarget
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘RcisTarget’ ...
** this is package ‘RcisTarget’ version ‘1.28.1’
** 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 (RcisTarget)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(RcisTarget)
> 
> test_check("RcisTarget")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
 38.644   6.053  44.059