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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:packFinder.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings packFinder_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/packFinder.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 ‘packFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘packFinder’ version ‘1.18.0’
* 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 ‘packFinder’ 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 ... 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) readBlast.Rd:100: Lost braces
   100 | code{\link{blastAnalysis}}, code{\link{blastAnnotate}},
       |     ^
checkRd: (-1) readBlast.Rd:100: Lost braces
   100 | code{\link{blastAnalysis}}, code{\link{blastAnnotate}},
       |                                 ^
checkRd: (-1) readBlast.Rd:101: Lost braces
   101 | code{\link{packAlign}}, 
       |     ^
checkRd: (-1) readBlast.Rd:102: Lost braces
   102 | code{\link{readUc}}, code{\link{packClust}}
       |     ^
checkRd: (-1) readBlast.Rd:102: Lost braces
   102 | code{\link{readUc}}, code{\link{packClust}}
       |                          ^
checkRd: (-1) readUc.Rd:98: Lost braces
    98 | code{\link{tirClust}}, code{\link{packAlign}}, 
       |     ^
checkRd: (-1) readUc.Rd:98: Lost braces
    98 | code{\link{tirClust}}, code{\link{packAlign}}, 
       |                            ^
checkRd: (-1) readUc.Rd:99: Lost braces
    99 | code{\link{readBlast}}, code{\link{packClust}}
       |     ^
checkRd: (-1) readUc.Rd:99: Lost braces
    99 | code{\link{readBlast}}, code{\link{packClust}}
       |                             ^
checkRd: (-1) tirClust.Rd:86: Lost braces
    86 | code{\link{packClust}}, code{\link{packAlign}},
       |     ^
checkRd: (-1) tirClust.Rd:86: Lost braces
    86 | code{\link{packClust}}, code{\link{packAlign}},
       |                             ^
* 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 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
arabidopsisThalianaRefseq 8.291  0.298  10.582
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/packFinder.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL packFinder
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘packFinder’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (packFinder)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(packFinder)
> 
> test_check("packFinder")
DNAStringSet object of length 1:
      width seq                                             names               
[1] 3800001 GGTGTTAAAAGGTTCTTGAGTG...TAGTCAGGTTTCTAACAGAAAA Chr3
[1] "File successfully written to tempTestOutput/packMatches.csv"
[1] "FASTA written to tempTestOutput/packMatches.fasta"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
  6.696   0.400   7.077