Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the DEScan2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEScan2.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. |
Package 484/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEScan2 1.12.0 (landing page) Dario Righelli
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: DEScan2 |
Version: 1.12.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEScan2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DEScan2_1.12.0.tar.gz |
StartedAt: 2021-10-14 22:09:38 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:20:57 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 679.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DEScan2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEScan2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DEScan2_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DEScan2.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'DEScan2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DEScan2' version '1.12.0' * 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 'DEScan2' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE .addScoreCol: no visible global function definition for 'mcols<-' Undefined global functions or variables: mcols<- * 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 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/DEScan2/libs/i386/DEScan2.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/DEScan2/libs/x64/DEScan2.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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed finalRegions 26.30 0.03 26.35 findPeaks 20.93 1.80 22.73 binnedCoverage 14.64 1.40 16.25 findOverlapsOverSamples 13.25 0.00 13.25 countFinalRegions 5.11 0.59 5.91 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findPeaks 28.31 2.32 30.64 finalRegions 30.14 0.08 30.22 findOverlapsOverSamples 17.13 0.00 17.12 binnedCoverage 11.60 1.45 13.22 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DEScan2.Rcheck/00check.log' for details.
DEScan2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DEScan2_1.12.0.tar.gz && rm -rf DEScan2.buildbin-libdir && mkdir DEScan2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEScan2.buildbin-libdir DEScan2_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DEScan2_1.12.0.zip && rm DEScan2_1.12.0.tar.gz DEScan2_1.12.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 57 2462k 57 1419k 0 0 2549k 0 --:--:-- --:--:-- --:--:-- 2549k 100 2462k 100 2462k 0 0 2923k 0 --:--:-- --:--:-- --:--:-- 2921k install for i386 * installing *source* package 'DEScan2' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpparma_max_win.cpp -o rcpparma_max_win.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o DEScan2.dll tmp.def RcppExports.o rcpparma_max_win.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DEScan2.buildbin-libdir/00LOCK-DEScan2/00new/DEScan2/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'DEScan2' finding HTML links ... done DEScan2 html RleListToRleMatrix html binToChrCoordMatRowNames html binnedCovOnly html binnedCoverage html c_get_disjoint_max_win html computeCoverageMovingWindowOnChr html computeLambdaOnChr html computeZ html constructBedRanges html countFinalRegions html createGranges html cutGRangesPerChromosome html divideEachSampleByChromosomes html evenRunMean html evenRunSum html finalRegions html findOverlapsOverSamples html findPeaks html fromSamplesToChrsGRangesList html generateDFofSamplesPerChromosomes html get_disjoint_max_win html giveUniqueNamesToPeaksOverSamples html initMergedPeaksNames html keepRelevantChrs html rcpparma_get_disjoint_max_win html readBamAsBed html readBedFile html readFilesAsGRangesList html saveGRangesAsBed html saveGRangesAsTsv html setGRGenomeInfo html ** 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 install for x64 * installing *source* package 'DEScan2' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpparma_max_win.cpp -o rcpparma_max_win.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o DEScan2.dll tmp.def RcppExports.o rcpparma_max_win.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DEScan2.buildbin-libdir/DEScan2/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'DEScan2' as DEScan2_1.12.0.zip * DONE (DEScan2) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'DEScan2' successfully unpacked and MD5 sums checked
DEScan2.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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("DEScan2") Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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 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 > > test_check("DEScan2") Maximizing with zthresh: 10 sigwin: 10 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 48.37 3.14 52.17 |
DEScan2.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" 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("DEScan2") Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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 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 > > test_check("DEScan2") Maximizing with zthresh: 10 sigwin: 10 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 53.23 2.46 55.98 |
DEScan2.Rcheck/examples_i386/DEScan2-Ex.timings
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DEScan2.Rcheck/examples_x64/DEScan2-Ex.timings
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