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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RcisTarget.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings RcisTarget_1.27.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/RcisTarget.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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 'RcisTarget/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RcisTarget' version '1.27.0'
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: 'doMC'
* 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 'RcisTarget' can be installed ... OK
* checking installed package size ... INFO
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
* 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) 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
addSignificantGenes     17.20   2.32   19.50
addMotifAnnotation      17.58   1.17   21.70
aucScores-class         10.49   0.97   11.42
getMotifAnnotation       9.04   0.75    9.77
reRank                   8.63   0.61    9.24
rankingRcisTarget-class  7.59   0.48    8.08
* 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: 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/RcisTarget.Rcheck/00check.log'
for details.