Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:00 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 chromstaR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromstaR.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 325/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chromstaR 1.24.0 (landing page) Aaron Taudt
| 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: chromstaR |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings chromstaR_1.24.0.tar.gz |
StartedAt: 2023-04-10 19:41:48 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:52:24 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 636.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: chromstaR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:chromstaR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings chromstaR_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/chromstaR.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘chromstaR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘chromstaR’ 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 ‘chromstaR’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.8Mb 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 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 ... 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 ... 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 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed combineMultivariates 21.359 0.284 21.644 enrichment_analysis 12.272 0.624 16.541 callPeaksMultivariate 10.744 0.472 11.215 callPeaksReplicates 8.982 0.248 9.230 unis2pseudomulti 8.019 0.200 8.222 plotGenomeBrowser 7.206 0.208 7.414 Chromstar 6.271 0.627 40.804 changePostCutoff 6.342 0.152 6.494 combinatorialStates 5.139 0.096 5.235 plotExpression 2.117 0.104 5.287 * 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 ... ‘chromstaR.Rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/chromstaR.Rcheck/00check.log’ for details.
chromstaR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL chromstaR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘chromstaR’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_interface.cpp -o R_interface.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c densities.cpp -o densities.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c init.cpp -o init.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c scalehmm.cpp -o scalehmm.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c utility.cpp -o utility.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-chromstaR/00new/chromstaR/libs ** 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 ** 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 (chromstaR)
chromstaR.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > library(testthat) > library(chromstaR) Loading required package: GenomicRanges Loading required package: stats4 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: ggplot2 Loading required package: chromstaRData Please visit https://github.com/ataudt/chromstaR for the latest bugfixes and features. > > test_check("chromstaR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ] > > proc.time() user system elapsed 19.651 0.779 20.412
chromstaR.Rcheck/chromstaR-Ex.timings
name | user | system | elapsed | |
Chromstar | 6.271 | 0.627 | 40.804 | |
binReads | 0.552 | 0.032 | 0.585 | |
callPeaksMultivariate | 10.744 | 0.472 | 11.215 | |
callPeaksReplicates | 8.982 | 0.248 | 9.230 | |
callPeaksUnivariate | 1.752 | 0.031 | 1.783 | |
changeMaxPostCutoff | 3.967 | 0.140 | 4.108 | |
changePostCutoff | 6.342 | 0.152 | 6.494 | |
collapseBins | 0.478 | 0.008 | 0.487 | |
combinatorialStates | 5.139 | 0.096 | 5.235 | |
combineMultivariates | 21.359 | 0.284 | 21.644 | |
conversion | 0 | 0 | 0 | |
enrichment_analysis | 12.272 | 0.624 | 16.541 | |
experiment.table | 0.003 | 0.000 | 0.003 | |
exportFiles | 1.124 | 0.032 | 1.156 | |
exportGRangesAsBedFile | 0.809 | 0.028 | 0.837 | |
fixedWidthBins | 0.064 | 0.004 | 0.068 | |
genes_rn4 | 0.108 | 0.000 | 0.108 | |
genomicFrequencies | 0.199 | 0.016 | 0.214 | |
getCombinations | 0.214 | 0.032 | 0.246 | |
getDistinctColors | 0.031 | 0.012 | 0.043 | |
getStateColors | 0.013 | 0.000 | 0.013 | |
heatmapCombinations | 0.469 | 0.012 | 0.480 | |
heatmapCountCorrelation | 0.361 | 0.020 | 0.381 | |
heatmapTransitionProbs | 0.363 | 0.004 | 0.367 | |
loadHmmsFromFiles | 1.656 | 0.068 | 1.724 | |
model.combined | 0.273 | 0.012 | 0.284 | |
model.multivariate | 0.216 | 0.004 | 0.219 | |
model.univariate | 0.069 | 0.008 | 0.077 | |
multiHMM | 0.198 | 0.012 | 0.210 | |
plotExpression | 2.117 | 0.104 | 5.287 | |
plotGenomeBrowser | 7.206 | 0.208 | 7.414 | |
plotHistogram | 2.613 | 0.176 | 2.789 | |
readBamFileAsGRanges | 0.633 | 0.016 | 0.649 | |
readBedFileAsGRanges | 1.307 | 0.032 | 1.342 | |
readCustomBedFile | 3.553 | 0.068 | 3.621 | |
removeCondition | 1.071 | 0.032 | 1.103 | |
state.brewer | 0.008 | 0.000 | 0.008 | |
stateBrewer | 0.029 | 0.000 | 0.029 | |
transitionFrequencies | 0.308 | 0.008 | 0.316 | |
unis2pseudomulti | 8.019 | 0.200 | 8.222 | |
variableWidthBins | 1.694 | 0.040 | 1.734 | |