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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:similaRpeak.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings similaRpeak_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/similaRpeak.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 ‘similaRpeak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘similaRpeak’ version ‘1.38.0’
* 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 ‘similaRpeak’ 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) DiffPosMax.Rd:64-65: Lost braces
    64 | \item \code{getMetric} { A function that returns the value of the
       |                        ^
checkRd: (-1) DiffPosMax.Rd:66-67: Lost braces
    66 | \item \code{getInfo} { A function that returns a description of the metric
       |                      ^
checkRd: (-1) DiffPosMax.Rd:68-69: Lost braces
    68 | \item \code{getType} { A function that returns the unique name associated
       |                      ^
checkRd: (-1) DiffPosMax.Rd:70-72: Lost braces
    70 | \item \code{calculateMetric} { A function that modifies the values of the
       |                              ^
checkRd: (-1) DiffPosMax.Rd:78-79: Lost braces
    78 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) Metric.Rd:32-33: Lost braces
    32 | \item \code{getMetric} { A function that returns the value of the
       |                        ^
checkRd: (-1) Metric.Rd:34-35: Lost braces
    34 | \item \code{getInfo} { A function that returns a description of the metric
       |                      ^
checkRd: (-1) Metric.Rd:36-37: Lost braces
    36 | \item \code{getType} { A function that returns the unique name associated
       |                      ^
checkRd: (-1) Metric.Rd:38-40: Lost braces
    38 | \item \code{calculateMetric} { A function that modifies the values of the
       |                              ^
checkRd: (-1) Metric.Rd:46-47: Lost braces
    46 | \item \code{\link{MetricFactory}} {for using the recommanded interface to 
       |                                   ^
checkRd: (-1) MetricFactory.Rd:44-45: Lost braces
    44 | \item \code{ratioAreaThreshold} { The minimum denominator accepted to 
       |                                 ^
checkRd: (-1) MetricFactory.Rd:46-48: Lost braces
    46 | \item \code{ratioMaxMaxThreshold} { The minimum denominator accepted to 
       |                                   ^
checkRd: (-1) MetricFactory.Rd:49-51: Lost braces
    49 | \item \code{ratioIntersectThreshold} { The minimum denominator accepted to 
       |                                      ^
checkRd: (-1) MetricFactory.Rd:52-54: Lost braces
    52 | \item \code{ratioIntersectThreshold} { The minimum denominator accepted to 
       |                                      ^
checkRd: (-1) MetricFactory.Rd:55-56: Lost braces
    55 | \item \code{diffPosMaxThresholdMinValue} { The minimum peak accepted to 
       |                                          ^
checkRd: (-1) MetricFactory.Rd:57-59: Lost braces
    57 | \item \code{diffPosMaxThresholdMaxDiff} { The maximum distance accepted 
       |                                         ^
checkRd: (-1) MetricFactory.Rd:60-61: Lost braces
    60 | \item \code{diffPosMaxTolerance} {The maximum variation accepted on the 
       |                                  ^
checkRd: (-1) MetricFactory.Rd:62-64: Lost braces
    62 | \item\code{spearmanCorrSDThreashold} {The minimum standard deviation 
       |                                      ^
checkRd: (-1) MetricFactory.Rd:118-119: Lost braces
   118 | \item \code{\link{similarity}} {for calculating all available metrics 
       |                                ^
checkRd: (-1) MetricFactory.Rd:120-121: Lost braces
   120 | \item \code{\link{demoProfiles}} {for more informations about ChIP-Seq
       |                                  ^
checkRd: (-1) RatioArea.Rd:43-44: Lost braces
    43 | \item \code{getMetric} { A function that returns the value of the
       |                        ^
checkRd: (-1) RatioArea.Rd:45-46: Lost braces
    45 | \item \code{getInfo} { A function that returns a description of the metric
       |                      ^
checkRd: (-1) RatioArea.Rd:47-48: Lost braces
    47 | \item \code{getType} { A function that returns the unique name associated
       |                      ^
checkRd: (-1) RatioArea.Rd:49-51: Lost braces
    49 | \item \code{calculateMetric} { A function that modifies the values of the
       |                              ^
checkRd: (-1) RatioArea.Rd:57-58: Lost braces
    57 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) RatioIntersect.Rd:43-44: Lost braces
    43 | \item \code{getMetric} { A function that returns the value of the
       |                        ^
checkRd: (-1) RatioIntersect.Rd:45-46: Lost braces
    45 | \item \code{getInfo} { A function that returns a description of the metric
       |                      ^
checkRd: (-1) RatioIntersect.Rd:47-48: Lost braces
    47 | \item \code{getType} { A function that returns the unique name associated
       |                      ^
checkRd: (-1) RatioIntersect.Rd:49-51: Lost braces
    49 | \item \code{calculateMetric} { A function that modifies the values of the
       |                              ^
checkRd: (-1) RatioIntersect.Rd:57-58: Lost braces
    57 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) RatioMaxMax.Rd:44-45: Lost braces
    44 | \item \code{getMetric} { A function that returns the value of the
       |                        ^
checkRd: (-1) RatioMaxMax.Rd:46-47: Lost braces
    46 | \item \code{getInfo} { A function that returns a description of the metric
       |                      ^
checkRd: (-1) RatioMaxMax.Rd:48-49: Lost braces
    48 | \item \code{getType} { A function that returns the unique name associated
       |                      ^
checkRd: (-1) RatioMaxMax.Rd:50-52: Lost braces
    50 | \item \code{calculateMetric} { A function that modifies the values of the
       |                              ^
checkRd: (-1) RatioMaxMax.Rd:58-59: Lost braces
    58 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) RatioNormalizedIntersect.Rd:45-46: Lost braces
    45 | \item \code{getMetric} { A function that returns the value of the
       |                        ^
checkRd: (-1) RatioNormalizedIntersect.Rd:47-48: Lost braces
    47 | \item \code{getInfo} { A function that returns a description of the metric
       |                      ^
checkRd: (-1) RatioNormalizedIntersect.Rd:49-50: Lost braces
    49 | \item \code{getType} { A function that returns the unique name associated
       |                      ^
checkRd: (-1) RatioNormalizedIntersect.Rd:51-53: Lost braces
    51 | \item \code{calculateMetric} { A function that modifies the values of the
       |                              ^
checkRd: (-1) RatioNormalizedIntersect.Rd:59-60: Lost braces
    59 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) SpearmanCorrelation.Rd:44-45: Lost braces
    44 | \item \code{getMetric} { A function that returns the value of the
       |                        ^
checkRd: (-1) SpearmanCorrelation.Rd:46-47: Lost braces
    46 | \item \code{getInfo} { A function that returns a description of the metric
       |                      ^
checkRd: (-1) SpearmanCorrelation.Rd:48-49: Lost braces
    48 | \item \code{getType} { A function that returns the unique name associated
       |                      ^
checkRd: (-1) SpearmanCorrelation.Rd:50-52: Lost braces
    50 | \item \code{calculateMetric} { A function that modifies the values of the
       |                              ^
checkRd: (-1) SpearmanCorrelation.Rd:58-59: Lost braces
    58 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) chr7Profiles.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chr7Profiles.Rd:16-17: Lost braces
    16 | \item \code{chr7Profiles$chr7.61968807.61969730} { a \code{list} containing  
       |                                                  ^
checkRd: (-1) chr7Profiles.Rd:18-21: Lost braces
    18 | \item \code{demoProfiles$chr7.61968807.61969730$H3K27ac} { a numeric vector 
       |                                                          ^
checkRd: (-1) chr7Profiles.Rd:22-25: Lost braces
    22 | \item \code{demoProfiles$chr7.61968807.61969730$H3K4me1} { a numeric vector 
       |                                                          ^
checkRd: (-1) chr7Profiles.Rd:68-69: Lost braces
    68 | \item \code{\link{demoProfiles}} { ChIP-seq profiles related to enhancers 
       |                                  ^
checkRd: (-1) chr7Profiles.Rd:70-71: Lost braces
    70 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) chr7Profiles.Rd:72-73: Lost braces
    72 | \item \code{\link{similarity}} {for calculating all available metrics 
       |                                ^
checkRd: (-1) demoProfiles.Rd:15-16: Lost braces
    15 | \item \code{demoProfiles} { a \code{list} containing all demo ChIP-Seq 
       |                           ^
checkRd: (-1) demoProfiles.Rd:17-18: Lost braces
    17 | \item \code{demoProfiles$chr2.70360770.70361098} { a list containing 2 
       |                                                  ^
checkRd: (-1) demoProfiles.Rd:19-22: Lost braces
    19 | \item \code{demoProfiles$chr2.70360770.70361098$H3K27ac} { a numeric vector 
       |                                                          ^
checkRd: (-1) demoProfiles.Rd:23-26: Lost braces
    23 | \item \code{demoProfiles$chr2.70360770.70361098$H3K4me1} { a numeric vector 
       |                                                          ^
checkRd: (-1) demoProfiles.Rd:27-28: Lost braces
    27 | \item \code{demoProfiles$chr3.73159773.73160145$H3K4me1} { a list containing 
       |                                                          ^
checkRd: (-1) demoProfiles.Rd:29-32: Lost braces
    29 | \item \code{demoProfiles$chr3.73159773.73160145$H3K27ac} { a numeric vector 
       |                                                          ^
checkRd: (-1) demoProfiles.Rd:33-36: Lost braces
    33 | \item \code{demoProfiles$chr3.73159773.73160145$H3K4me1} { a numeric vector 
       |                                                          ^
checkRd: (-1) demoProfiles.Rd:72-74: Lost braces
    72 | \item \code{\link{chr7Profiles}} { ChIP-Seq profiles of region 
       |                                  ^
checkRd: (-1) demoProfiles.Rd:75-76: Lost braces
    75 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) demoProfiles.Rd:77-78: Lost braces
    77 | \item \code{\link{similarity}} {for calculating all available metrics 
       |                                ^
checkRd: (-1) diffPosMaxMethod.Rd:42-43: Lost braces
    42 | \item \code{\link{MetricFactory}} {for using the recommanded interface to 
       |                                   ^
checkRd: (-1) ratioAreaMethod.Rd:34-35: Lost braces
    34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to 
       |                                   ^
checkRd: (-1) ratioIntersectMethod.Rd:34-35: Lost braces
    34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to 
       |                                   ^
checkRd: (-1) ratioMaxMaxMethod.Rd:34-35: Lost braces
    34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to 
       |                                   ^
checkRd: (-1) similaRpeak-package.Rd:39-40: Lost braces
    39 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) similaRpeak-package.Rd:41-42: Lost braces
    41 | \item \code{\link{similarity}} {for calculating all available metrics 
       |                                ^
checkRd: (-1) similarity.Rd:160-161: Lost braces
   160 | \item \code{\link{MetricFactory}} {for using a interface to calculate all 
       |                                   ^
checkRd: (-1) similarity.Rd:162-163: Lost braces
   162 | \item \code{\link{demoProfiles}} {for more informations about ChIP-Seq
       |                                  ^
checkRd: (-1) spearmanCorrMethod.Rd:34-35: Lost braces
    34 | \item \code{\link{MetricFactory}} {for using the recommanded interface to 
       |                                   ^
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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/similaRpeak.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL similaRpeak
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘similaRpeak’ ...
** 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 (similaRpeak)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> ## Run all tests in the similaRpeak package
> BiocGenerics:::testPackage("similaRpeak")
Metric type: RATIO_MAX_MAX. Metric value: NA
Metric type: NA. Metric value: NA


RUNIT TEST PROTOCOL -- Wed Nov 20 02:48:08 2024 
*********************************************** 
Number of test functions: 85 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
similaRpeak RUnit Tests - 85 test functions, 0 errors, 0 failures
Number of test functions: 85 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In max(profile1, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In max(profile2, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
> 
> 
> proc.time()
   user  system elapsed 
  0.477   0.074   0.552