Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-16 12:04 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4867 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4655 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4600 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 769/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FRASER 2.5.2 (landing page) Christian Mertes
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 2.5.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FRASER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FRASER_2.5.2.tar.gz |
StartedAt: 2025-10-15 22:15:57 -0400 (Wed, 15 Oct 2025) |
EndedAt: 2025-10-15 22:41:30 -0400 (Wed, 15 Oct 2025) |
EllapsedTime: 1532.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FRASER.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FRASER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FRASER_2.5.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FRASER.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FRASER/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FRASER’ version ‘2.5.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 34 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘FRASER’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.1.sdk’ * 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 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’ estimateBestQ: no visible binding for global variable ‘oht’ hyperParams: no visible binding for global variable ‘oht’ loadFraserDataSet: no visible global function definition for ‘slotNames’ plotEncDimSearch.FRASER: no visible binding for global variable ‘oht’ plotEncDimSearch.FRASER: no visible binding for global variable ‘singular_values’ plotVolcano.FRASER: no visible binding for global variable ‘aberrantLabel’ updateSeqlevelsStyle: no visible binding for global variable ‘NCBI_Genome_Name’ updateSeqlevelsStyle: no visible global function definition for ‘setNames’ updateSeqlevelsStyle: no visible global function definition for ‘seqnames<-’ updateSeqlevelsStyle: no visible binding for global variable ‘UCSC_Genome_Name’ plotEncDimSearch,FraserDataSet: no visible binding for global variable ‘oht’ plotEncDimSearch,FraserDataSet: no visible binding for global variable ‘singular_values’ 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: NCBI_Genome_Name UCSC_Genome_Name aberrantLabel gene_rowIdx include oht pValueGene padjust padjustGene seqnames<- setNames singular_values slotNames Consider adding importFrom("methods", "slotNames") importFrom("stats", "setNames") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plotFunctions.Rd: aberrant Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 is not available * 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 182.205 19.987 241.557 potentialImpactAnnotations 109.493 3.920 127.642 FRASER 45.003 1.253 52.510 results 29.825 1.000 33.813 mergeExternalData 27.350 2.355 31.255 injectOutliers 26.655 0.228 27.946 annotateRanges 24.518 1.143 36.631 estimateBestQ 24.578 0.309 25.335 calculatePSIValues 22.780 0.519 23.750 filtering 20.553 0.345 23.365 fds-methods 20.464 0.409 22.603 getter_setter_functions 20.266 0.310 20.767 subset 19.866 0.310 20.359 counts 19.221 0.292 19.765 createTestFraserDataSet 16.962 0.395 18.888 makeSimulatedFraserDataSet 4.434 0.045 5.247 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/FRASER.Rcheck/00check.log’ for details.
FRASER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FRASER ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘FRASER’ ... ** this is package ‘FRASER’ version ‘2.5.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DARMA_DONT_USE_OPENMP -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DARMA_DONT_USE_OPENMP -fPIC -falign-functions=64 -Wall -g -O2 -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FRASER.so RcppExports.o loss_n_gradient_functions.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-FRASER/00new/FRASER/libs ** 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 ** 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 (FRASER)
FRASER.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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: Seqinfo Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: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 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 > > # to speed up the testing on windows do it in serial mode > if(.Platform$OS.type != "unix") { + register(SerialParam()) + } > > test_check("FRASER") Optimal encoding dimension: 2 Optimal encoding dimension: 2 [ FAIL 0 | WARN 248 | SKIP 0 | PASS 106 ] [ FAIL 0 | WARN 248 | SKIP 0 | PASS 106 ] > > proc.time() user system elapsed 238.888 73.894 270.848
FRASER.Rcheck/FRASER-Ex.timings
name | user | system | elapsed | |
FRASER | 45.003 | 1.253 | 52.510 | |
FraserDataSet | 0.496 | 0.028 | 0.540 | |
annotateRanges | 24.518 | 1.143 | 36.631 | |
calculatePSIValues | 22.780 | 0.519 | 23.750 | |
countRNA | 1.096 | 0.031 | 1.144 | |
counts | 19.221 | 0.292 | 19.765 | |
createTestFraserDataSet | 16.962 | 0.395 | 18.888 | |
estimateBestQ | 24.578 | 0.309 | 25.335 | |
fds-methods | 20.464 | 0.409 | 22.603 | |
filtering | 20.553 | 0.345 | 23.365 | |
getter_setter_functions | 20.266 | 0.310 | 20.767 | |
injectOutliers | 26.655 | 0.228 | 27.946 | |
loadFraserDataSet | 0.362 | 0.012 | 0.592 | |
makeSimulatedFraserDataSet | 4.434 | 0.045 | 5.247 | |
mergeExternalData | 27.350 | 2.355 | 31.255 | |
plotFunctions | 182.205 | 19.987 | 241.557 | |
potentialImpactAnnotations | 109.493 | 3.920 | 127.642 | |
psiTypes | 0.000 | 0.001 | 0.001 | |
results | 29.825 | 1.000 | 33.813 | |
subset | 19.866 | 0.310 | 20.359 | |