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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:benchdamic.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings benchdamic_1.12.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/benchdamic.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'benchdamic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'benchdamic' version '1.12.2'
* 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 'benchdamic' 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 ... NOTE
Namespace in Imports field not imported from: 'microbiome'
  All declared Imports should be used.
* 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) DA_Seurat.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:33-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:47-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:64-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:68-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:71-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) areaCAT.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:24-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:83-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:20-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:24-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:31-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractDA.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractDA.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractDA.Rd:67-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getDA.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getDA.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getDA.Rd:63-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_counts_metadata.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_counts_metadata.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_counts_metadata.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotConcordance.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotConcordance.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) set_Seurat.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:31-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:43-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:72: Lost braces in \itemize; meant \describe ?
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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
DA_ALDEx2       8.83   2.34   12.75
DA_ANCOM        3.23   2.39  380.99
plotConcordance 5.47   0.12    5.61
DA_DESeq2       3.89   0.03    6.38
DA_Seurat       2.13   0.00   17.13
DA_corncob      1.27   0.06    5.55
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/benchdamic.Rcheck/00check.log'
for details.