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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GenomicFiles.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GenomicFiles_1.42.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GenomicFiles.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 ‘GenomicFiles/DESCRIPTION’ ... OK
* this is package ‘GenomicFiles’ version ‘1.42.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'MatrixGenerics', 'GenomicRanges',
  'SummarizedExperiment', 'BiocParallel', 'Rsamtools', 'rtracklayer'
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 ‘GenomicFiles’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
checkRd: (5) GenomicFiles-class.Rd:40-43: \item in \describe must have non-empty label
checkRd: (5) VcfStack-class.Rd:61-89: \item in \describe must have non-empty label
checkRd: (5) VcfStack-class.Rd:90-105: \item in \describe must have non-empty label
checkRd: (5) pack-methods.Rd:57-61: \item in \describe must have non-empty label
checkRd: (-1) reduceByFile-methods.Rd:132-139: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceByFile-methods.Rd:140-143: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceByRange-methods.Rd:143-150: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceByRange-methods.Rd:151-154: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) registry-utils.Rd:45-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registry-utils.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registry-utils.Rd:64-68: 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
reduceByFile-methods  8.493  4.327   5.686
reduceByRange-methods 7.700  4.533   7.661
GenomicFiles-class    6.155  1.461   6.174
VcfStack-class        5.424  2.051   8.353
reduceByYield         4.286  1.628  24.730
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘GenomicFiles_unit_tests.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: 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GenomicFiles.Rcheck/00check.log’
for details.