##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromstaR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings chromstaR_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/chromstaR.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'chromstaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chromstaR' version '1.33.1'
* 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 whether package 'chromstaR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
  installed size is  5.5Mb
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  binReads.Rd: GRanges-class
  callPeaksUnivariate.Rd: GRanges-class
  callPeaksUnivariateAllChr.Rd: GRanges-class
  enrichmentAtAnnotation.Rd: GRanges-class
  enrichment_analysis.Rd: GRanges-class
  exportGRangesAsBedFile.Rd: GRanges-class
  fixedWidthBins.Rd: GRanges-class
  plotExpression.Rd: GRanges-class, ggplot2
  readBamFileAsGRanges.Rd: GRanges-class
  readBedFileAsGRanges.Rd: GRanges-class
  readCustomBedFile.Rd: GRanges-class
  subsample.Rd: GRanges-class
  variableWidthBins.Rd: GRanges-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/chromstaR/libs/x64/chromstaR.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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  21.68   0.97   23.06
enrichment_analysis   18.95   0.95   21.68
callPeaksMultivariate 10.53   0.25   10.97
callPeaksReplicates    9.27   0.36    9.73
unis2pseudomulti       8.44   0.30    8.74
plotGenomeBrowser      7.96   0.11    8.06
Chromstar              6.48   0.31   45.11
combinatorialStates    6.34   0.28    6.62
changePostCutoff       6.27   0.22    6.49
readCustomBedFile      5.76   0.11    5.87
plotExpression         4.06   0.27    5.49
* 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: 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/chromstaR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL chromstaR
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'chromstaR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c R_interface.cpp -o R_interface.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c densities.cpp -o densities.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c init.cpp -o init.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c scalehmm.cpp -o scalehmm.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c utility.cpp -o utility.o
g++ -std=gnu++17 -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-chromstaR/00new/chromstaR/libs/x64
** 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
Warning in fun(libname, pkgname) :
  Package 'chromstaR' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'chromstaR' is deprecated and will be removed from Bioconductor
  version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (chromstaR)

R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: chromstaRData
Warning message:
In fun(libname, pkgname) :
  Package 'chromstaR' is deprecated and will be removed from Bioconductor
  version 3.22
> 
> test_check("chromstaR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
  19.01    0.70   19.73