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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scanMiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scanMiR_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scanMiR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scanMiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scanMiR’ version ‘1.13.0’
* 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 ‘scanMiR’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 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 ... NOTE
.aggregateSiteInfo: no visible binding for global variable ‘ORF’
.aggregateSiteInfo: no visible global function definition for ‘.’
.aggregateSiteInfo: no visible binding for global variable
  ‘ORF.canonical’
.aggregateSiteInfo: no visible binding for global variable
  ‘ORF.nonCanonical’
.aggregateSiteInfo: no visible binding for global variable ‘..cols’
.aggregate_miRNA: no visible binding for global variable ‘ORF’
.aggregate_miRNA: no visible binding for global variable ‘log_kd’
.aggregate_miRNA: no visible binding for global variable ‘orf.length’
.aggregate_miRNA: no visible binding for global variable ‘utr.length’
.aggregate_miRNA: no visible binding for global variable ‘utr_score’
.aggregate_miRNA: no visible binding for global variable ‘orf_score’
dummyKdData: no visible binding for global variable ‘SampleKdModel’
plotKdModel: no visible binding for global variable ‘seed’
plotKdModel: no visible binding for global variable ‘log_kd’
viewTargetAlignment: no visible binding for global variable ‘x’
viewTargetAlignment: no visible binding for global variable ‘y’
viewTargetAlignment: no visible binding for global variable ‘label’
Undefined global functions or variables:
  . ..cols ORF ORF.canonical ORF.nonCanonical SampleKdModel label
  log_kd orf.length orf_score seed utr.length utr_score x y
* checking Rd files ... NOTE
checkRd: (-1) plotKdModel.Rd:28: Lost braces
    28 | [seqLogo]{https://bioconductor.org/packages/release/bioc/html/seqLogo.html}
       |          ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aggregateMatches.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/scanMiR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scanMiR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘scanMiR’ ...
** 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 (scanMiR)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(scanMiR)
> 
> test_check("scanMiR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
> 
> proc.time()
   user  system elapsed 
  8.971   0.458   9.533