Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-27 11:36:31 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4667 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4403 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4426 |
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 |
Package 345/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
chromstaR 1.28.0 (landing page) Aaron Taudt
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the chromstaR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: chromstaR |
Version: 1.28.0 |
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromstaR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings chromstaR_1.28.0.tar.gz |
StartedAt: 2024-03-25 23:23:38 -0400 (Mon, 25 Mar 2024) |
EndedAt: 2024-03-25 23:31:06 -0400 (Mon, 25 Mar 2024) |
EllapsedTime: 448.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: chromstaR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromstaR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings chromstaR_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/chromstaR.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'chromstaR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'chromstaR' version '1.28.0' * 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 whether package 'chromstaR' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 12.3.0' * checking installed package size ... NOTE installed size is 5.5Mb 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 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 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 for x64 is not available File 'F:/biocbuild/bbs-3.18-bioc/R/library/chromstaR/libs/x64/chromstaR.dll': Found '_assert', possibly from 'assert' (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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'chromstaR-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotExpression > ### Title: Overlap with expression data > ### Aliases: plotExpression > > ### ** Examples > > ## Load an example multiHMM > file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData", + package="chromstaR") > model <- get(load(file)) > > ## Obtain expression data > data(expression_lv) > head(expression_lv) ensembl_gene_id expression_BN expression_SHR 1 ENSRNOG00000000001 8.8 7.4 2 ENSRNOG00000000007 20.0 13.0 3 ENSRNOG00000000008 1.8 3.4 4 ENSRNOG00000000010 6.2 506.8 5 ENSRNOG00000000012 48.0 36.4 6 ENSRNOG00000000014 18.2 15.2 > > ## We need to get coordinates for each of the genes > library(biomaRt) > ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') Ensembl site unresponsive, trying asia mirror Ensembl site unresponsive, trying useast mirror Error in .chooseEnsemblMirror(mirror = mirror, httr_config = httr_config) : Unable to query any Ensembl site Calls: useEnsembl -> .chooseEnsemblMirror Execution halted * 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 ERROR, 3 NOTEs See 'F:/biocbuild/bbs-3.18-bioc/meat/chromstaR.Rcheck/00check.log' for details.
chromstaR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL chromstaR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'chromstaR' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o g++ -std=gnu++17 -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-chromstaR/00new/chromstaR/libs/x64 ** 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 ** 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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" Copyright (C) 2024 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(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 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: 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 19.59 0.84 20.46
chromstaR.Rcheck/chromstaR-Ex.timings
name | user | system | elapsed | |
Chromstar | 6.52 | 0.26 | 43.92 | |
binReads | 0.50 | 0.05 | 0.57 | |
callPeaksMultivariate | 10.07 | 0.44 | 10.65 | |
callPeaksReplicates | 9.79 | 0.35 | 10.28 | |
callPeaksUnivariate | 2.12 | 0.04 | 2.16 | |
changeMaxPostCutoff | 4.8 | 0.2 | 5.0 | |
changePostCutoff | 6.40 | 0.20 | 6.61 | |
collapseBins | 0.52 | 0.00 | 0.52 | |
combinatorialStates | 5.51 | 0.28 | 5.79 | |
combineMultivariates | 21.24 | 0.35 | 21.96 | |
conversion | 0 | 0 | 0 | |
enrichment_analysis | 17.92 | 0.65 | 26.31 | |
experiment.table | 0.00 | 0.02 | 0.01 | |
exportFiles | 1.06 | 0.05 | 1.11 | |
exportGRangesAsBedFile | 0.83 | 0.00 | 0.83 | |
fixedWidthBins | 0.10 | 0.01 | 0.11 | |
genes_rn4 | 0.10 | 0.03 | 0.14 | |
genomicFrequencies | 0.21 | 0.00 | 0.20 | |
getCombinations | 0.28 | 0.00 | 0.29 | |
getDistinctColors | 0.08 | 0.00 | 0.07 | |
getStateColors | 0.01 | 0.00 | 0.02 | |
heatmapCombinations | 0.5 | 0.0 | 0.5 | |
heatmapCountCorrelation | 0.38 | 0.03 | 0.41 | |
heatmapTransitionProbs | 0.44 | 0.00 | 0.43 | |
loadHmmsFromFiles | 2.45 | 0.10 | 2.58 | |
model.combined | 0.26 | 0.01 | 0.28 | |
model.multivariate | 0.24 | 0.02 | 0.25 | |
model.univariate | 0.09 | 0.00 | 0.10 | |
multiHMM | 0.22 | 0.01 | 0.23 | |