##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chromstaR_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/chromstaR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.25.0’
* 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 ‘chromstaR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used SDK: ‘’
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
* 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 R 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 startup messages can be suppressed ... 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
Chromstar: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
combineMultivariates  32.672  0.486  48.918
enrichment_analysis   29.308  1.050  46.663
plotGenomeBrowser     17.953  0.107  26.985
callPeaksMultivariate 15.160  0.278  21.009
callPeaksReplicates   12.765  0.208  17.689
unis2pseudomulti      11.735  0.153  17.560
changePostCutoff      11.188  0.183  15.002
Chromstar              9.847  0.350  90.033
combinatorialStates    9.133  0.163  13.116
changeMaxPostCutoff    7.848  0.140  10.828
readCustomBedFile      6.709  0.098  10.206
plotHistogram          4.252  0.064   6.393
plotExpression         3.863  0.095   7.283
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/meat/chromstaR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chromstaR
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘chromstaR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include    -fPIC  -Wall -g -O2  -c R_interface.cpp -o R_interface.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include    -fPIC  -Wall -g -O2  -c densities.cpp -o densities.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include    -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include    -fPIC  -Wall -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include    -fPIC  -Wall -g -O2  -c utility.cpp -o utility.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-chromstaR/00new/chromstaR/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chromstaR)

R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> library(testthat)
> library(chromstaR)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: chromstaRData

Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features.

> 
> test_check("chromstaR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
 29.374   1.082  45.815