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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HIVcDNAvantWout03.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HIVcDNAvantWout03_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/HIVcDNAvantWout03.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘HIVcDNAvantWout03/DESCRIPTION’ ... OK
* this is package ‘HIVcDNAvantWout03’ version ‘1.46.0’
* 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 ‘HIVcDNAvantWout03’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
* checking package 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 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 Rd files ... OK
* 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 ... NOTE
Output for data("hiv1raw", package = "HIVcDNAvantWout03"):
  Read 450000 items
Output for data("hiv2raw", package = "HIVcDNAvantWout03"):
  Read 450000 items
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘hivData.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... NONE
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/HIVcDNAvantWout03.Rcheck/00check.log’
for details.