##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:bnbc.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings bnbc_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/bnbc.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bnbc/DESCRIPTION’ ... OK
* this is package ‘bnbc’ version ‘1.24.0’
* 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 ‘bnbc’ can be installed ... WARNING
Found the following significant warnings:
  Warning: cooler_methods.Rd:58: unexpected macro '\dontrun'
  Warning: cooler_methods.Rd:75: unexpected '}'
  Warning: cooler_methods.Rd:59: All text must be in a section
  Warning: cooler_methods.Rd:60: All text must be in a section
  Warning: cooler_methods.Rd:62: All text must be in a section
  Warning: cooler_methods.Rd:64: All text must be in a section
  Warning: cooler_methods.Rd:66: All text must be in a section
  Warning: cooler_methods.Rd:67: All text must be in a section
  Warning: cooler_methods.Rd:68: All text must be in a section
  Warning: cooler_methods.Rd:69: All text must be in a section
  Warning: cooler_methods.Rd:70: All text must be in a section
  Warning: cooler_methods.Rd:71: All text must be in a section
  Warning: cooler_methods.Rd:72: All text must be in a section
  Warning: cooler_methods.Rd:73: All text must be in a section
  Warning: cooler_methods.Rd:74: All text must be in a section
See ‘/home/biocbuild/bbs-3.18-bioc/meat/bnbc.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    cooler   2.9Mb
    data     2.4Mb
    libs     1.6Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘HiCBricks’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getChrCGFromCools: no visible global function definition for
  ‘Create_many_Bricks_from_mcool’
getChrCGFromCools: no visible global function definition for
  ‘Brick_load_data_from_mcool’
getChrCGFromCools: no visible global function definition for
  ‘Brick_get_entire_matrix’
getChrCGFromCools: no visible global function definition for
  ‘h5closeAll’
Undefined global functions or variables:
  Brick_get_entire_matrix Brick_load_data_from_mcool
  Create_many_Bricks_from_mcool h5closeAll
* checking Rd files ... WARNING
checkRd: (5) ContactGroup-class.Rd:72-74: \item in \describe must have non-empty label
prepare_Rd: cooler_methods.Rd:58: unexpected macro '\dontrun'
prepare_Rd: cooler_methods.Rd:75: unexpected '}'
prepare_Rd: cooler_methods.Rd:59: All text must be in a section
prepare_Rd: cooler_methods.Rd:60: All text must be in a section
prepare_Rd: cooler_methods.Rd:62: All text must be in a section
prepare_Rd: cooler_methods.Rd:64: All text must be in a section
prepare_Rd: cooler_methods.Rd:66: All text must be in a section
prepare_Rd: cooler_methods.Rd:67: All text must be in a section
prepare_Rd: cooler_methods.Rd:68: All text must be in a section
prepare_Rd: cooler_methods.Rd:69: All text must be in a section
prepare_Rd: cooler_methods.Rd:70: All text must be in a section
prepare_Rd: cooler_methods.Rd:71: All text must be in a section
prepare_Rd: cooler_methods.Rd:72: All text must be in a section
prepare_Rd: cooler_methods.Rd:73: All text must be in a section
prepare_Rd: cooler_methods.Rd:74: All text must be in a section
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'cooler_methods':
getChrIdx
  Code: function(chr.length, step, chr)
  Docs: function(chr.length, step)
  Argument names in code not in docs:
    chr
getChrCGFromCools
  Code: function(files, chr, step, index.gr, work.dir, exp.name,
                 coldata, norm.factor = NULL)
  Docs: function(files, chr, step, index.gr, work.dir, exp.name,
                 coldata)
  Argument names in code not in docs:
    norm.factor

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'cooler_methods':
  ‘getChrIdx’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘bnbc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bnbc
> ### Title: Normalize Contact Matrices with BNBC
> ### Aliases: bnbc
> 
> ### ** Examples
> 
> data(cgEx)
> batches <- colData(cgEx)$Batch
> cgEx.cpm <- logCPM(cgEx)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 ERROR, 4 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/bnbc.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL bnbc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘bnbc’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c update_bands.cpp -o update_bands.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o bnbc.so RcppExports.o update_bands.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-bnbc/00new/bnbc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: cooler_methods.Rd:58: unexpected macro '\dontrun'
Warning: cooler_methods.Rd:75: unexpected '}'
Warning: cooler_methods.Rd:59: All text must be in a section
Warning: cooler_methods.Rd:60: All text must be in a section
Warning: cooler_methods.Rd:62: All text must be in a section
Warning: cooler_methods.Rd:64: All text must be in a section
Warning: cooler_methods.Rd:66: All text must be in a section
Warning: cooler_methods.Rd:67: All text must be in a section
Warning: cooler_methods.Rd:68: All text must be in a section
Warning: cooler_methods.Rd:69: All text must be in a section
Warning: cooler_methods.Rd:70: All text must be in a section
Warning: cooler_methods.Rd:71: All text must be in a section
Warning: cooler_methods.Rd:72: All text must be in a section
Warning: cooler_methods.Rd:73: All text must be in a section
Warning: cooler_methods.Rd:74: All text must be in a section
*** 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 (bnbc)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.

> require("bnbc") || stop("unable to load bnbc")
Loading required package: bnbc
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: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

[1] TRUE
> BiocGenerics:::testPackage("bnbc")


RUNIT TEST PROTOCOL -- Thu Nov  2 08:56:58 2023 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bnbc RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 16.469   1.319  19.496