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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NestLink_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/NestLink.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘NestLink/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NestLink’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'AnnotationHub', 'ExperimentHub', 'Biostrings', 'gplots', 'protViz',
  'ShortRead'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘NestLink’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with no role:
  Damien Morger <damien.morger@rqmicro.com>
* 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 whether startup messages can be suppressed ... 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) runNGSAnalysis.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runNGSAnalysis.Rd:35: 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
runNGSAnalysis           129.848  1.100 131.266
getExperimentHubFilename  12.120  0.876  15.468
getFC                      4.836  0.132   5.456
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/NestLink.Rcheck/00check.log’
for details.