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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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scanMiR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.12.0’
* 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 ... 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
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/scanMiR.Rcheck/00check.log’
for details.