##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plotgardener.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings plotgardener_1.11.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/plotgardener.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'plotgardener/DESCRIPTION' ... OK
* this is package 'plotgardener' version '1.11.3'
* package encoding: UTF-8
* 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 'plotgardener' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* 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
.checkCool: no visible binding for global variable 'name'
pgParams: no visible binding for global variable 'width'
pgParams: no visible binding for global variable 'strand'
Undefined global functions or variables:
  name strand width
* checking Rd files ... NOTE
checkRd: (-1) annoDomains.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoHeatmapLegend.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoHeatmapLegend.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoXaxis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoXaxis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoYaxis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoYaxis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotIdeogram.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotIdeogram.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLegend.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLegend.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMultiSignal.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMultiSignal.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairs.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairs.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSignal.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSignal.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:91-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:70: Lost braces in \itemize; meant \describe ?
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/plotgardener/libs/x64/plotgardener.dll':
  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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'plotgardener-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readCool
> ### Title: Read a .(m)cool file and return Hi-C data as a dataframe
> ### Aliases: readCool
> 
> ### ** Examples
> 
> 
> ## .cool file
> coolFile <- file.path(tempdir(), "Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool")
> download.file(url = "https://usgs2.osn.mghpcc.org/cooler01/examples/hg19/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool",
+     destfile = coolFile)
trying URL 'https://usgs2.osn.mghpcc.org/cooler01/examples/hg19/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool'
Content type 'binary/octet-stream' length 4103444 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

> 
> ## Read in region `chr2:10000000-22000000` at 1000Kb cool file resolution
> coolData <- readCool(file = coolFile, chrom = "chr2", chromstart = 10000000,
+                      chromend = 22000000,
+                      resolution = 1000000)
Error in `.checkCool()`:
! File must be a `.cool` or `.mcool` file
✖ C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpWo0Q4X/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool is not in HDF5 format
Backtrace:
    ▆
 1. └─plotgardener::readCool(...)
 2.   └─plotgardener:::.checkCoolErrors(...)
 3.     └─plotgardener:::.checkCool(file)
 4.       └─rlang::abort(c("File must be a `.cool` or `.mcool` file", x = glue("{file} is not in HDF5 format")))
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-readingFunctions.R:92:5'): readCool ────────────────────────────
  Error in `.checkCool(file = coolFile)`: File must be a `.cool` or `.mcool` file
  x C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgndjDg/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool is not in HDF5 format
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(.checkCool(file = coolFile), ".cool") at test-readingFunctions.R:92:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─plotgardener:::.checkCool(file = coolFile)
   5.   └─rlang::abort(c("File must be a `.cool` or `.mcool` file", x = glue("{file} is not in HDF5 format")))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/plotgardener.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL plotgardener
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'plotgardener' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c checkRow.cpp -o checkRow.o
g++ -std=gnu++17  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rebinBigwig.cpp -o rebinBigwig.o
g++ -std=gnu++17 -shared -s -static-libgcc -o plotgardener.dll tmp.def RcppExports.o checkRow.o rebinBigwig.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-plotgardener/00new/plotgardener/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plotgardener)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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(plotgardener)

Attaching package: 'plotgardener'

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

    c

> 
> test_check("plotgardener")
Loading required package: GenomicFeatures
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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: GenomicRanges
Loading required package: AnnotationDbi
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")'.


Using poppler version 23.08.0
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    cache

pairs[pairs1]
arches[arches1]
ranges[ranges1]
transcripts[transcripts1]
start, endLoading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Read in hic file with KR normalization at 1e+05 BP resolution.
trying URL 'https://usgs2.osn.mghpcc.org/cooler01/examples/hg19/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool'
Content type 'binary/octet-stream' length 4103444 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

signal[signal1_h]
signal[signal1_h]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-readingFunctions.R:92:5'): readCool ────────────────────────────
Error in `.checkCool(file = coolFile)`: File must be a `.cool` or `.mcool` file
x C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpgndjDg/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool is not in HDF5 format
Backtrace:
    ▆
 1. ├─testthat::expect_equal(.checkCool(file = coolFile), ".cool") at test-readingFunctions.R:92:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─plotgardener:::.checkCool(file = coolFile)
 5.   └─rlang::abort(c("File must be a `.cool` or `.mcool` file", x = glue("{file} is not in HDF5 format")))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]
Error: Test failures
Execution halted