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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:isomiRs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings isomiRs_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/isomiRs.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘isomiRs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘isomiRs’ version ‘1.35.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘isomiRs’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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
.clean_noise: no visible binding for global variable ‘total’
.clean_noise: no visible binding for global variable ‘hits’
.remove_gt_n_changes: no visible binding for global variable ‘changes’
isoAnnotate: no visible binding for global variable ‘pct’
isoCounts: no visible global function definition for ‘as.tibble’
isoPlot: no visible global function definition for ‘across’
isoPlot: no visible global function definition for ‘everything’
isoPlot: no visible binding for global variable ‘iso_sample’
isoPlotPosition: no visible global function definition for ‘across’
isoPlotPosition: no visible global function definition for ‘everything’
isoPlotPosition: no visible binding for global variable ‘iso_sample’
isoSelect.IsomirDataSeq: no visible global function definition for
  ‘across’
isoSelect.IsomirDataSeq: no visible global function definition for
  ‘everything’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Hs.egMIRNA’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Hs.egMIRBASE2FAMILY’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Hs.egTARGETS’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Hs.egTARGETSFULL’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Mm.egMIRNA’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Mm.egMIRBASE2FAMILY’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Mm.egTARGETS’
mirna2targetscan: no visible binding for global variable
  ‘targetscan.Mm.egTARGETSFULL’
isoSelect,IsomirDataSeq: no visible global function definition for
  ‘across’
isoSelect,IsomirDataSeq: no visible global function definition for
  ‘everything’
Undefined global functions or variables:
  across as.tibble changes everything hits iso_sample pct
  targetscan.Hs.egMIRBASE2FAMILY targetscan.Hs.egMIRNA
  targetscan.Hs.egTARGETS targetscan.Hs.egTARGETSFULL
  targetscan.Mm.egMIRBASE2FAMILY targetscan.Mm.egMIRNA
  targetscan.Mm.egTARGETS targetscan.Mm.egTARGETSFULL total
* 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 ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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-3.21-bioc/meat/isomiRs.Rcheck/00check.log’
for details.