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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cleaver.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cleaver_1.49.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/cleaver.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cleaver/DESCRIPTION’ ... OK
* this is package ‘cleaver’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 ‘cleaver’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 1 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 2 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 3 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 4 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 5 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 6 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 7 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 8 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 9 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 10 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 11 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 12 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 13 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 14 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 15 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 16 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 17 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 18 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 19 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 20 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 21 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 22 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 23 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 24 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 25 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 26 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 27 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 28 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 29 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 30 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 31 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 32 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 33 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 34 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 35 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 36 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 37 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 38 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 39 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 40 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 41 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 42 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 43 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 44 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 45 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 46 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 47 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 48 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 49 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 50 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 51 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 52 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 53 has 7)
checkRd: (-1) cleave-methods.Rd:117-184: Only 8 columns allowed in this table (row 54 has 7)
checkRd: (-1) cleave-methods.Rd:187-198: Only 8 columns allowed in this table (row 2 has 7)
checkRd: (-1) cleave-methods.Rd:187-198: Only 8 columns allowed in this table (row 6 has 7)
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'cleaver-package.Rd':
  ‘[cleaver:cleave-methods]{cleave}’
  ‘[cleaver:cleave-methods]{cleavageRanges}’
  ‘[cleaver:cleave-methods]{cleavageSites}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cleave-methods.Rd: AAString-class, AAStringSet-class,
    AAStringSetList-class, IRanges-class, IRangesList-class
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 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-3.23-bioc/meat/cleaver.Rcheck/00check.log’
for details.