Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2238/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VariantFiltering 1.42.0 (landing page) Robert Castelo
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the VariantFiltering package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantFiltering.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: VariantFiltering |
Version: 1.42.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantFiltering.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantFiltering_1.42.0.tar.gz |
StartedAt: 2024-12-21 12:57:59 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 13:07:21 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 561.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: VariantFiltering.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantFiltering.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantFiltering_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/VariantFiltering.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VariantFiltering/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantFiltering’ version ‘1.42.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘VariantFiltering’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: R 1.1Mb extdata 3.7Mb * 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:::labeledLine' 'VariantAnnotation:::.checkArgs' 'VariantAnnotation:::.consolidateHits' 'VariantAnnotation:::.returnEmpty' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.adjustForStrandSense' '.ancestorsSO' '.findSOIDs' * 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 ... 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 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 VariantFilteringParam-class 8.626 2.503 13.14 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/VariantFiltering.Rcheck/00check.log’ for details.
VariantFiltering.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VariantFiltering ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘VariantFiltering’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o methods-WeightMatrix.c:341:9: warning: variable 'line' set but not used [-Wunused-but-set-variable] int line=1; ^ methods-WeightMatrix.c:546:11: warning: variable 'line' set but not used [-Wunused-but-set-variable] int line=1; ^ 2 warnings generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-VariantFiltering/00new/VariantFiltering/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 (VariantFiltering)
VariantFiltering.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > BiocGenerics:::testPackage("VariantFiltering") 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min 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 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname 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: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5 Loading OrgDb annotation package org.Hs.eg.db Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene Assuming the genome build of the input variants is hs37d5. Switching to the UCSC chromosome-name style from the transcript-centric annotation package. Chromosome chrM has different lengths between the input VCF and the input TxDb pakage. This chromosome will be discarded from further analysis Assumming hs37d5 and hg19 represent the same genome build. Discarding scaffold sequences. Annotating variant type (SNV, Insertion, Deletion, MNV, Delins) Annotating location with VariantAnnotation::locateVariants() Annotating coding variants VariantAnnotation::predictCoding() Annotating codon usage frequencies in coding synonymous variants Scoring binding sites with weight matrix donorSites. Scoring binding sites with weight matrix acceptorSites. 1000 variants processed RUNIT TEST PROTOCOL -- Sat Dec 21 13:07:08 2024 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : VariantFiltering RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 Warning messages: 1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 597 out-of-bound ranges located on sequences 29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222, 72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544, 73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674, 76675, 76676, 76677, 76679, and 76680. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 2: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style 3: In annotationEngine(variants, param, annotationCache, BPPARAM = BPPARAM) : Assumming GRCh37.p13 and hs37d5 represent the same genome build. 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 597 out-of-bound ranges located on sequences 29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222, 72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544, 73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674, 76675, 76676, 76677, 76679, and 76680. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 5: In .scoreBindingSiteVariants(variantsVR_annotated, weightMatrices, : Assumming GRCh37.p13 and hs37d5 represent the same genome build. 6: In recycleSingleBracketReplacementValue(value, x, nsbs) : number of values supplied is not a sub-multiple of the number of values to be replaced 7: In recycleSingleBracketReplacementValue(value, x, nsbs) : number of values supplied is not a sub-multiple of the number of values to be replaced > > proc.time() user system elapsed 94.331 5.882 107.975
VariantFiltering.Rcheck/VariantFiltering-Ex.timings
name | user | system | elapsed | |
GenePhylostrataDb-class | 0 | 0 | 0 | |
VariantFilteringParam-class | 8.626 | 2.503 | 13.140 | |
VariantFilteringResults-class | 0.000 | 0.001 | 0.004 | |
VariantType-class | 0.001 | 0.000 | 0.001 | |
WeightMatrix-class | 0.010 | 0.004 | 0.016 | |
autosomalDominant | 0 | 0 | 0 | |
autosomalRecessiveHeterozygous | 0 | 0 | 0 | |
autosomalRecessiveHomozygous | 0 | 0 | 0 | |
deNovo | 0.000 | 0.000 | 0.001 | |
readAAradicalChangeMatrix | 0.005 | 0.001 | 0.011 | |
unrelatedIndividuals | 0 | 0 | 0 | |
xLinked | 0 | 0 | 0 | |