Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:21 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 bsseq package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 225/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bsseq 1.35.0 (landing page) Kasper Daniel Hansen
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
Package: bsseq |
Version: 1.35.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bsseq.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings bsseq_1.35.0.tar.gz |
StartedAt: 2022-12-28 22:09:06 -0500 (Wed, 28 Dec 2022) |
EndedAt: 2022-12-28 22:18:56 -0500 (Wed, 28 Dec 2022) |
EllapsedTime: 589.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: bsseq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bsseq.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings bsseq_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/bsseq.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'bsseq/DESCRIPTION' ... OK * this is package 'bsseq' version '1.35.0' * 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 'bsseq' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 12.2.0' * 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 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 ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'DelayedArray:::get_verbose_block_processing' 'DelayedArray:::normarg_grid' 'GenomicRanges:::.extract_groups_from_GenomicRanges' 'GenomicRanges:::.get_circle_length' 'GenomicRanges:::extraColumnSlotNames' 'IRanges:::.shift_ranges_in_groups_to_first_circle' 'S4Vectors:::normarg_names' 'S4Vectors:::numeric2integer' 'S4Vectors:::sapply_isNULL' 'data.table:::funique' See the note in ?`:::` about the use of this operator. * 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 ... WARNING Missing link or links in documentation object 'BSmooth.Rd': 'BatchJobsParam-class' Missing link or links in documentation object 'read.bismark.Rd': 'BatchJobsParam-class' See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.17-bioc/R/library/bsseq/libs/x64/bsseq.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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getMeth 6.78 1.88 8.80 findLoci 6.39 0.15 6.54 getCoverage 5.89 0.09 6.32 BSmooth.tstat 5.31 0.23 5.89 BSseq-class 3.36 0.13 27.36 read.bismark 0.78 0.03 11.47 * 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: • Skipping tests that require SnowParam with multiple machines (1) • TODO: Remove these tests if no longer required (1) • empty test (4) ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_BSmooth.R:64'): Expected parallelisation backends work with in-memory realization backend ── Error in `BatchJobsParam(2, progressbar = FALSE)`: could not find function "BatchJobsParam" Backtrace: ▆ 1. └─bsseq::BSmooth(bsseq_test, BPPARAM = BatchJobsParam(2, progressbar = FALSE)) at test_BSmooth.R:64:8 2. └─methods::is(BPPARAM, "SnowParam") [ FAIL 1 | WARN 6 | SKIP 6 | PASS 131 ] Error: Test failures Execution halted * 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, 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/bsseq.Rcheck/00check.log' for details.
bsseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL bsseq ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'bsseq' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/beachmat/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_M_and_Cov.cpp -o check_M_and_Cov.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/beachmat/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/beachmat/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-bsseq/00new/bsseq/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 (bsseq)
bsseq.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 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(bsseq) 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: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors 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: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > test_check("bsseq") [ FAIL 1 | WARN 6 | SKIP 6 | PASS 131 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • Skipping tests that require SnowParam with multiple machines (1) • TODO: Remove these tests if no longer required (1) • empty test (4) ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_BSmooth.R:64'): Expected parallelisation backends work with in-memory realization backend ── Error in `BatchJobsParam(2, progressbar = FALSE)`: could not find function "BatchJobsParam" Backtrace: ▆ 1. └─bsseq::BSmooth(bsseq_test, BPPARAM = BatchJobsParam(2, progressbar = FALSE)) at test_BSmooth.R:64:8 2. └─methods::is(BPPARAM, "SnowParam") [ FAIL 1 | WARN 6 | SKIP 6 | PASS 131 ] Error: Test failures Execution halted
bsseq.Rcheck/bsseq-Ex.timings
name | user | system | elapsed | |
BS.chr22 | 0.91 | 0.02 | 0.94 | |
BSmooth | 0 | 0 | 0 | |
BSmooth.fstat | 0 | 0 | 0 | |
BSmooth.tstat | 5.31 | 0.23 | 5.89 | |
BSseq-class | 3.36 | 0.13 | 27.36 | |
BSseq | 0.39 | 0.06 | 0.54 | |
FWGRanges-class | 0 | 0 | 0 | |
computeStat | 0 | 0 | 0 | |
data.frame2GRanges | 0.02 | 0.00 | 0.02 | |
dmrFinder | 1.17 | 0.01 | 1.20 | |
findLoci | 6.39 | 0.15 | 6.54 | |
fisherTests | 0.38 | 0.01 | 0.43 | |
getCoverage | 5.89 | 0.09 | 6.32 | |
getMeth | 6.78 | 1.88 | 8.80 | |
getStats | 0.27 | 0.09 | 0.36 | |
goodnessOfFit | 3.31 | 0.19 | 3.50 | |
hasGRanges-class | 0 | 0 | 0 | |
read.bismark | 0.78 | 0.03 | 11.47 | |
read.umtab | 0 | 0 | 0 | |
smoothSds | 0 | 0 | 0 | |