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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylInheritance_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/methylInheritance.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 ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.30.0’
* 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 ‘methylInheritance’ 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 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) demoForTransgenerationalAnalysis.Rd:59-61: Lost braces
    59 |     \item \code{\link{runPermutation}} {for running a
       |                                        ^
checkRd: (-1) demoForTransgenerationalAnalysis.Rd:62-63: Lost braces
    62 |     \item \code{\link{runObservation}} {for running an
       |                                        ^
checkRd: (-1) isInterGenerationResults.Rd:21: Lost braces; missing escapes or markup?
    21 | "_permutation_{permutationID}.RDS" extension.}
       |               ^
checkRd: (-1) methylInheritance-package.Rd:19-21: Lost braces
    19 |     \item \code{\link{runPermutation}} {for running a
       |                                        ^
checkRd: (-1) methylInheritance-package.Rd:22-23: Lost braces
    22 |     \item \code{\link{runObservation}} {for running an
       |                                        ^
checkRd: (-1) methylInheritanceResults.Rd:293-294: Lost braces
   293 |     \item \code{\link{extractInfo}} {for extracting the
       |                                     ^
checkRd: (-1) readInterGenerationResults.Rd:25: Lost braces; missing escapes or markup?
    25 | "_permutation_{permutationID}.RDS" extension.}
       |               ^
checkRd: (-1) runOnePermutationOnAllGenerations.Rd:144-173: Lost braces
   144 | itemize{
       |        ^
checkRd: (-1) samplesForTransgenerationalAnalysis.Rd:48-50: Lost braces
    48 |     \item \code{\link{runPermutation}} {for running a
       |                                        ^
checkRd: (-1) saveInterGenerationResults.Rd:27: Lost braces; missing escapes or markup?
    27 | "_permutation_{permutationID}.RDS" extension.}
       |               ^
* 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
runPermutation                      91.251  1.283  93.040
runObservation                      39.140  0.613  39.919
samplesForTransgenerationalAnalysis 28.455  0.467  29.008
runOnePermutationOnAllGenerations   10.406  0.197  10.658
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/methylInheritance.Rcheck/00check.log’
for details.