Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 61/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
amplican 1.27.0 (landing page) Eivind Valen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the amplican package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/amplican.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: amplican |
Version: 1.27.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:amplican.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings amplican_1.27.0.tar.gz |
StartedAt: 2024-06-09 23:32:32 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 23:38:55 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 382.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: amplican.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:amplican.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings amplican_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/amplican.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'amplican/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'amplican' version '1.27.0' * 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 'amplican' 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 ... 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 There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'get_seq' * 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 ... NOTE checkRd: (-1) amplicanAlign.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:65-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:60-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:107-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:60-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:107-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanSummarize.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanSummarize.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:53-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:74-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:77-78: Lost braces in \itemize; meant \describe ? * 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 ... NOTE Documented arguments not in \usage in Rd file 'getEventInfo.Rd': 'ampl_len' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/amplican/libs/x64/amplican.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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed amplicanAlign 6.42 1.46 7.92 amplicanPipeline 6.65 0.22 7.16 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/amplican.Rcheck/00check.log' for details.
amplican.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL amplican ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'amplican' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bezier.cpp -o bezier.o g++ -std=gnu++17 -shared -s -static-libgcc -o amplican.dll tmp.def RcppExports.o bezier.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-amplican/00new/amplican/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 (amplican)
amplican.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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(amplican) 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: Biostrings Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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:grDevices': windows Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: pwalign Attaching package: 'pwalign' The following objects are masked from 'package:Biostrings': PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned, alignedPattern, alignedSubject, compareStrings, deletion, errorSubstitutionMatrices, indel, insertion, mismatchSummary, mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix, pairwiseAlignment, pid, qualitySubstitutionMatrices, stringDist, unaligned, writePairwiseAlignments Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second version: 1.27.0 Please consider supporting this software by citing: Labun et al. 2019 Accurate analysis of genuine CRISPR editing events with ampliCan. Genome Res. 2019 Mar 8 doi: 10.1101/gr.244293.118 > > test_check("amplican") [ FAIL 0 | WARN 11 | SKIP 0 | PASS 57 ] [ FAIL 0 | WARN 11 | SKIP 0 | PASS 57 ] > > proc.time() user system elapsed 25.60 9.48 35.50
amplican.Rcheck/amplican-Ex.timings
name | user | system | elapsed | |
AlignmentsExperimentSet-class | 1.33 | 0.14 | 1.47 | |
amplicanAlign | 6.42 | 1.46 | 7.92 | |
amplicanConsensus | 0.10 | 0.01 | 0.12 | |
amplicanFilter | 0.04 | 0.00 | 0.05 | |
amplicanMap | 0.34 | 0.01 | 0.36 | |
amplicanNormalize | 0.05 | 0.00 | 0.05 | |
amplicanOverlap | 0.03 | 0.00 | 0.03 | |
amplicanPipeline | 6.65 | 0.22 | 7.16 | |
amplicanReport | 0.02 | 0.00 | 0.28 | |
amplicanSummarize | 0.00 | 0.02 | 0.03 | |
amplican_print_reads | 0.28 | 0.00 | 0.29 | |
assignedCount | 0.03 | 0.00 | 0.03 | |
barcodeData-set | 0 | 0 | 0 | |
barcodeData | 0 | 0 | 0 | |
comb_along | 0.02 | 0.00 | 0.02 | |
experimentData-set | 0 | 0 | 0 | |
experimentData | 0.01 | 0.00 | 0.01 | |
extractEvents | 2.39 | 0.02 | 2.41 | |
findEOP | 0.02 | 0.00 | 0.02 | |
findLQR | 0.00 | 0.01 | 0.01 | |
findPD | 0.00 | 0.02 | 0.02 | |
fwdReads-set | 0 | 0 | 0 | |
fwdReads | 0.33 | 0.01 | 0.34 | |
fwdReadsType-set | 0 | 0 | 0 | |
fwdReadsType | 0 | 0 | 0 | |
geom_bezier | 0.4 | 0.1 | 0.5 | |
lookupAlignment | 0.22 | 0.00 | 0.22 | |
metaplot_deletions | 0.33 | 0.00 | 0.32 | |
metaplot_insertions | 0.45 | 0.01 | 0.47 | |
metaplot_mismatches | 0.33 | 0.00 | 0.33 | |
plot_cuts | 0.27 | 0.00 | 0.27 | |
plot_deletions | 0.23 | 0.03 | 0.26 | |
plot_height | 0 | 0 | 0 | |
plot_heterogeneity | 0.19 | 0.05 | 0.24 | |
plot_insertions | 0.55 | 0.00 | 0.54 | |
plot_mismatches | 1.48 | 0.14 | 1.63 | |
plot_variants | 0.97 | 0.03 | 1.00 | |
readCounts-set | 0 | 0 | 0 | |
readCounts | 0 | 0 | 0 | |
rveReads-set | 0 | 0 | 0 | |
rveReads | 0.29 | 0.02 | 0.32 | |
rveReadsType-set | 0.02 | 0.00 | 0.01 | |
rveReadsType | 0 | 0 | 0 | |
unassignedCount | 0 | 0 | 0 | |
unassignedData-set | 0.01 | 0.00 | 0.02 | |
unassignedData | 0 | 0 | 0 | |
writeAlignments | 0.03 | 0.00 | 0.03 | |