| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:45 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1496/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| plotgardener 1.4.2 (landing page) Nicole Kramer
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: plotgardener |
| Version: 1.4.2 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plotgardener.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings plotgardener_1.4.2.tar.gz |
| StartedAt: 2023-04-11 04:35:16 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 04:40:54 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 337.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: plotgardener.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plotgardener.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings plotgardener_1.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/plotgardener.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'plotgardener/DESCRIPTION' ... OK
* this is package 'plotgardener' version '1.4.2'
* 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 'F:/biocbuild/bbs-3.16-bioc/R/library/plotgardener/libs/x64/plotgardener.dll':
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. 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 10.34 0.44 10.81
plotIdeogram 6.03 0.56 6.97
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/plotgardener.Rcheck/00check.log'
for details.
plotgardener.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL plotgardener ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'plotgardener' ... ** using staged installation ** libs g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c checkRow.cpp -o checkRow.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rebinBigwig.cpp -o rebinBigwig.o g++ -std=gnu++14 -shared -s -static-libgcc -o plotgardener.dll tmp.def RcppExports.o checkRow.o rebinBigwig.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-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)
plotgardener.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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, 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: 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.
signal[signal2]
signal[signal2]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 106 ]
>
> proc.time()
user system elapsed
32.32 1.95 34.98
plotgardener.Rcheck/plotgardener-Ex.timings
| name | user | system | elapsed | |
| annoDomains | 1.46 | 0.02 | 1.50 | |
| annoGenomeLabel | 3.71 | 0.11 | 3.81 | |
| annoHeatmapLegend | 0.57 | 0.02 | 0.58 | |
| annoHighlight | 0.84 | 0.00 | 0.84 | |
| annoPixels | 0.76 | 0.07 | 0.86 | |
| annoSegments | 4.43 | 0.10 | 4.52 | |
| annoText | 0.82 | 0.01 | 0.84 | |
| annoXaxis | 1.35 | 0.10 | 1.44 | |
| annoYaxis | 0.94 | 0.07 | 1.04 | |
| annoZoomLines | 3.78 | 0.24 | 4.01 | |
| assembly | 0 | 0 | 0 | |
| c | 0 | 0 | 0 | |
| calcSignalRange | 0.30 | 0.00 | 0.34 | |
| colorby | 0.48 | 0.03 | 0.52 | |
| defaultPackages | 0.02 | 0.00 | 0.02 | |
| genomes | 0 | 0 | 0 | |
| mapColors | 0.08 | 0.00 | 0.07 | |
| pageCreate | 0.03 | 0.00 | 0.04 | |
| pageGuideHide | 0.01 | 0.00 | 0.01 | |
| pageGuideHorizontal | 0.02 | 0.00 | 0.02 | |
| pageGuideShow | 0.72 | 0.05 | 0.76 | |
| pageGuideVertical | 0.06 | 0.00 | 0.06 | |
| pageLayoutCol | 0.02 | 0.00 | 0.02 | |
| pageLayoutRow | 0 | 0 | 0 | |
| pagePlotPlace | 0.56 | 0.03 | 0.59 | |
| pagePlotRemove | 0.39 | 0.01 | 0.41 | |
| pgParams | 1.14 | 0.11 | 1.25 | |
| plotCircle | 0.03 | 0.00 | 0.03 | |
| plotGG | 0.41 | 0.02 | 0.42 | |
| plotGenes | 3.83 | 0.12 | 3.96 | |
| plotGenomeLabel | 1.64 | 0.10 | 1.73 | |
| plotHicRectangle | 0.43 | 0.03 | 0.45 | |
| plotHicSquare | 0.62 | 0.03 | 0.66 | |
| plotHicTriangle | 2.24 | 0.03 | 2.26 | |
| plotIdeogram | 6.03 | 0.56 | 6.97 | |
| plotLegend | 0.29 | 0.21 | 0.50 | |
| plotManhattan | 3.15 | 0.20 | 3.35 | |
| plotMultiSignal | 1.59 | 0.06 | 1.66 | |
| plotPairs | 0.09 | 0.00 | 0.10 | |
| plotPairsArches | 0.10 | 0.00 | 0.09 | |
| plotPolygon | 0.01 | 0.02 | 0.03 | |
| plotRanges | 0.21 | 0.11 | 0.32 | |
| plotRaster | 10.34 | 0.44 | 10.81 | |
| plotRect | 0.42 | 0.00 | 0.42 | |
| plotSegments | 0.03 | 0.00 | 0.03 | |
| plotSignal | 0.73 | 0.04 | 0.78 | |
| plotText | 0.05 | 0.00 | 0.04 | |
| plotTranscripts | 0.88 | 0.05 | 0.93 | |
| readBigwig | 0 | 0 | 0 | |
| readHic | 0.00 | 0.00 | 0.02 | |