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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings chromstaR_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/chromstaR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.32.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is  5.8Mb
  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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
combineMultivariates  19.534  0.398  19.942
enrichment_analysis   12.497  0.925  15.486
callPeaksMultivariate  9.768  0.261  10.030
callPeaksReplicates    9.514  0.322   9.838
unis2pseudomulti       7.191  0.274   7.466
plotGenomeBrowser      6.653  0.263   6.919
combinatorialStates    5.856  0.193   6.050
Chromstar              5.708  0.190  37.864
changePostCutoff       5.407  0.215   5.622
plotExpression         2.841  0.242  14.023
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘chromstaR.Rnw’ using knitr

Quitting from lines 536-555 [combined_enrichment] (chromstaR.Rnw)
Error: processing vignette 'chromstaR.Rnw' failed with diagnostics:
Unable to query any Ensembl site
--- failed re-building ‘chromstaR.Rnw’

SUMMARY: processing the following file failed:
  ‘chromstaR.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/chromstaR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL chromstaR
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘chromstaR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c R_interface.cpp -o R_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c densities.cpp -o densities.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c scalehmm.cpp -o scalehmm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall  -c utility.cpp -o utility.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 16.241   0.844  17.074