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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ERSSA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ERSSA_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ERSSA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ERSSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ERSSA’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘ERSSA’ 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 ... NOTE
Namespace in Imports field not imported from: ‘apeglm’
  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) erssa.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:90-91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:92-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:95-97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) erssa.Rd:98-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_TPR_FPRPlot.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_TPR_FPRPlot.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_TPR_FPRPlot.Rd:35-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_dotplot.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_dotplot.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_dotplot.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_intersectPlot.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_marginPlot.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ggplot2_marginPlot.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
* 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
erssa_deseq2_parallel 28.540  0.396  28.937
erssa_deseq2          27.653  0.337  27.993
erssa                  9.256  0.242   9.487
* 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-3.20-bioc/meat/ERSSA.Rcheck/00check.log’
for details.