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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_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/chromstaR.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 ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.31.0’
* 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 ‘chromstaR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  5.3Mb
  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 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 whether 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 ... NOTE
checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces
    66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
       |                                              ^
checkRd: (-1) callPeaksUnivariate.Rd:66: Lost braces
    66 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
       |                                                                                                                                                                                   ^
checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces
    60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
       |                                              ^
checkRd: (-1) callPeaksUnivariateAllChr.Rd:60: Lost braces
    60 | \item{post.cutoff}{False discovery rate. code{NULL} means that the state with maximum posterior probability will be chosen, irrespective of its absolute probability (default=code{NULL}).}
       |                                                                                                                                                                                   ^
checkRd: (-1) plotGenomeBrowser.Rd:28-68: Lost braces
    28 | plotGenomeBrowser2 <- function(counts, peaklist=NULL, chr, start, end, countcol='black', peakcols=NULL, style='peaks', peakTrackHeight=5) {
       |                                                                                                                                           ^
checkRd: (-1) plotGenomeBrowser.Rd:36-41: Lost braces
    36 |     if (style == 'peaks') {
       |                           ^
checkRd: (-1) plotGenomeBrowser.Rd:41-45: Lost braces
    41 |     } else if (style == 'density') {
       |                                    ^
checkRd: (-1) plotGenomeBrowser.Rd:45-47: Lost braces
    45 |     } else {
       |            ^
checkRd: (-1) plotGenomeBrowser.Rd:50-65: Lost braces
    50 |     if (!is.null(peaklist)) {
       |                             ^
checkRd: (-1) plotGenomeBrowser.Rd:51-53: Lost braces
    51 |         if (is.null(peakcols)) {
       |                                ^
checkRd: (-1) plotGenomeBrowser.Rd:54-64: Lost braces
    54 |         for (i1 in 1:length(peaklist)) {
       |                                        ^
checkRd: (-1) plotGenomeBrowser.Rd:57-60: Lost braces
    57 |             if (length(peaks) > 0) {
       |                                    ^
* 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 ... ERROR
Running examples in ‘chromstaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichment_analysis
> ### Title: Enrichment analysis
> ### Aliases: enrichment_analysis plotFoldEnrichHeatmap
> ###   plotEnrichCountHeatmap plotEnrichment
> 
> ### ** Examples
> 
> ### Get an example multiHMM ###
> file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
+                     package="chromstaR")
> model <- get(load(file))
> 
> ### Obtain gene coordinates for rat from biomaRt ###
> library(biomaRt)
> ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl')
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
Error in .chooseEnsemblMirror(mirror = mirror, http_config = http_config) : 
  Unable to query any Ensembl site
Calls: useEnsembl -> .chooseEnsemblMirror
Execution halted
* 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: 1 ERROR, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘chromstaR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c R_interface.cpp -o R_interface.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c densities.cpp -o densities.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c init.cpp -o init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c scalehmm.cpp -o scalehmm.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utility.cpp -o utility.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.4-x86_64/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 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.

> 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

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 
 13.185   0.622  13.829