Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 738/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FRASER 2.1.0 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the FRASER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FRASER.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: FRASER |
Version: 2.1.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FRASER.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FRASER_2.1.0.tar.gz |
StartedAt: 2024-07-16 00:08:54 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 00:23:21 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 867.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FRASER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FRASER.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FRASER_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/FRASER.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'FRASER/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'FRASER' version '2.1.0' * 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 'FRASER' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'S4Vectors:::selectSome' 'ggbio:::.buildFacetsFromArgs' 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 ... NOTE annotateRangesWithTxDb: no visible binding for global variable 'include' calculatePadjValuesOnSubset : <anonymous>: no visible binding for global variable 'gene_rowIdx' plotVolcano.FRASER: no visible binding for global variable 'aberrantLabel' plotVolcano,FraserDataSet: no visible binding for global variable 'aberrantLabel' results,FraserDataSet: no visible binding for global variable 'padjust' results,FraserDataSet: no visible binding for global variable 'pValueGene' results,FraserDataSet: no visible binding for global variable 'padjustGene' Undefined global functions or variables: aberrantLabel gene_rowIdx include pValueGene padjust padjustGene * 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 x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/FRASER/libs/x64/FRASER.dll': Found '_exit', possibly from '_exit' (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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotFunctions 105.51 2.72 108.33 FRASER 32.82 1.29 34.98 potentialImpactAnnotations 32.11 0.83 32.90 injectOutliers 22.34 0.44 22.93 annotateRanges 20.05 0.65 31.39 results 16.66 0.33 16.97 mergeExternalData 15.89 0.31 16.79 optimHyperParams 15.33 0.20 15.77 filtering 13.02 1.78 14.86 fds-methods 13.00 0.64 13.73 createTestFraserDataSet 13.25 0.19 14.35 calculatePSIValues 12.95 0.25 13.20 getter_setter_functions 11.83 1.05 12.95 subset 11.68 0.36 12.11 counts 11.81 0.18 11.98 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/FRASER.Rcheck/00check.log' for details.
FRASER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL FRASER ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'FRASER' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o g++ -std=gnu++17 -shared -s -static-libgcc -o FRASER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRlapack -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-FRASER/00new/FRASER/libs/x64 ** R ** 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 (FRASER)
FRASER.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(FRASER) Loading required package: BiocParallel Loading required package: data.table Loading required package: Rsamtools Loading required package: GenomeInfoDb 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, 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:data.table': first, second 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:data.table': shift The following object is masked from 'package:grDevices': windows Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit 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 Attaching package: 'FRASER' The following object is masked from 'package:Biobase': samples The following object is masked from 'package:GenomeInfoDb': mapSeqlevels > > # to speed up the testing on windows do it in serial mode > if(.Platform$OS.type != "unix") { + register(SerialParam()) + } > > test_check("FRASER") ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.19.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || sample3.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : C:/Users/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid68488 ... || || Features : 87 || || Meta-features : 87 || || Chromosomes/contigs : 2 || || || || Process BAM file sample3.bam... || || Strand specific : stranded || || Paired-end reads are included. || || Total alignments : 1918 || || Successfully assigned alignments : 241 (12.6%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// [ FAIL 0 | WARN 672 | SKIP 0 | PASS 97 ] [ FAIL 0 | WARN 672 | SKIP 0 | PASS 97 ] > > proc.time() user system elapsed 121.12 5.20 132.98
FRASER.Rcheck/FRASER-Ex.timings
name | user | system | elapsed | |
FRASER | 32.82 | 1.29 | 34.98 | |
FraserDataSet | 0.31 | 0.03 | 0.41 | |
annotateRanges | 20.05 | 0.65 | 31.39 | |
calculatePSIValues | 12.95 | 0.25 | 13.20 | |
countRNA | 0.66 | 0.07 | 0.72 | |
counts | 11.81 | 0.18 | 11.98 | |
createTestFraserDataSet | 13.25 | 0.19 | 14.35 | |
fds-methods | 13.00 | 0.64 | 13.73 | |
filtering | 13.02 | 1.78 | 14.86 | |
getter_setter_functions | 11.83 | 1.05 | 12.95 | |
injectOutliers | 22.34 | 0.44 | 22.93 | |
loadFraserDataSet | 0.23 | 0.03 | 0.28 | |
makeSimulatedFraserDataSet | 2.94 | 0.08 | 3.02 | |
mergeExternalData | 15.89 | 0.31 | 16.79 | |
optimHyperParams | 15.33 | 0.20 | 15.77 | |
plotFunctions | 105.51 | 2.72 | 108.33 | |
potentialImpactAnnotations | 32.11 | 0.83 | 32.90 | |
psiTypes | 0 | 0 | 0 | |
results | 16.66 | 0.33 | 16.97 | |
subset | 11.68 | 0.36 | 12.11 | |