Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:08:18 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for plotgardener on riesling1


To the developers/maintainers of the plotgardener package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plotgardener.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1438/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plotgardener 1.1.16  (landing page)
Nicole Kramer
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/plotgardener
git_branch: master
git_last_commit: 4322d3a
git_last_commit_date: 2022-03-16 14:10:08 -0400 (Wed, 16 Mar 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: plotgardener
Version: 1.1.16
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plotgardener.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings plotgardener_1.1.16.tar.gz
StartedAt: 2022-03-17 19:53:22 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:58:07 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 285.2 seconds
RetCode: 0
Status:   OK  
CheckDir: plotgardener.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plotgardener.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings plotgardener_1.1.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/plotgardener.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plotgardener/DESCRIPTION' ... OK
* this is package 'plotgardener' version '1.1.16'
* 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
* 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 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 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 ... OK
* checking Rd files ... OK
* 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 'D:/biocbuild/bbs-3.15-bioc/R/library/plotgardener/libs/x64/plotgardener.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plotRaster   10.29   1.21   11.50
plotIdeogram  4.66   0.52    6.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/plotgardener.Rcheck/00check.log'
for details.



Installation output

plotgardener.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL plotgardener
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'plotgardener' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c checkRow.cpp -o checkRow.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rebinBigwig.cpp -o rebinBigwig.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o plotgardener.dll tmp.def RcppExports.o checkRow.o rebinBigwig.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-plotgardener/00new/plotgardener/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'plotgardener'
    finding HTML links ... done
    annoDomains                             html  
    annoGenomeLabel                         html  
    annoHeatmapLegend                       html  
    annoHighlight                           html  
    annoPixels                              html  
    annoSegments                            html  
    annoText                                html  
    annoXaxis                               html  
    annoYaxis                               html  
    annoZoomLines                           html  
    assembly                                html  
    c                                       html  
    colorby                                 html  
    defaultPackages                         html  
    genomes                                 html  
    mapColors                               html  
    pageCreate                              html  
    pageGuideHide                           html  
    pageGuideHorizontal                     html  
    pageGuideShow                           html  
    pageGuideVertical                       html  
    pagePlotPlace                           html  
    pagePlotRemove                          html  
    pgParams                                html  
    plotCircle                              html  
    plotGG                                  html  
    plotGenes                               html  
    plotGenomeLabel                         html  
    plotHicRectangle                        html  
    plotHicSquare                           html  
    plotHicTriangle                         html  
    plotIdeogram                            html  
    plotLegend                              html  
    plotManhattan                           html  
    plotPairs                               html  
    plotPairsArches                         html  
    plotPolygon                             html  
    plotRanges                              html  
    plotRaster                              html  
    plotRect                                html  
    plotSegments                            html  
    plotSignal                              html  
    plotText                                html  
    plotTranscripts                         html  
    plotgardener                            html  
    readBigwig                              html  
    readHic                                 html  
*** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RUVSeq' is missing or broken
 done

Tests output

plotgardener.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> 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, 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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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")'.


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.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 98 ]
> 
> proc.time()
   user  system elapsed 
  24.64    1.76   26.40 

Example timings

plotgardener.Rcheck/plotgardener-Ex.timings

nameusersystemelapsed
annoDomains0.890.111.00
annoGenomeLabel3.150.263.43
annoHeatmapLegend0.690.020.70
annoHighlight0.920.050.97
annoPixels1.890.142.03
annoSegments2.060.062.12
annoText0.730.000.73
annoXaxis0.950.111.06
annoYaxis0.830.050.88
annoZoomLines2.640.072.72
assembly000
c000
colorby0.470.040.50
defaultPackages000
genomes000
mapColors0.060.000.14
pageCreate0.030.010.05
pageGuideHide0.020.000.02
pageGuideHorizontal0.010.000.01
pageGuideShow0.890.030.92
pageGuideVertical0.060.000.07
pagePlotPlace0.540.020.54
pagePlotRemove0.450.090.55
pgParams0.810.080.89
plotCircle0.020.000.02
plotGG0.170.000.17
plotGenes3.690.053.73
plotGenomeLabel1.750.041.80
plotHicRectangle0.560.020.58
plotHicSquare0.820.050.86
plotHicTriangle1.430.071.52
plotIdeogram4.660.526.18
plotLegend0.360.140.52
plotManhattan2.130.142.27
plotPairs0.50.00.5
plotPairsArches0.10.00.1
plotPolygon0.010.000.01
plotRanges0.160.060.22
plotRaster10.29 1.2111.50
plotRect0.570.040.61
plotSegments0.040.000.05
plotSignal0.860.080.95
plotText0.050.000.05
plotTranscripts0.890.080.97
readBigwig000
readHic0.000.010.02