Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:46 -0400 (Wed, 21 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1952/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SingleMoleculeFootprinting 1.13.0 (landing page) Guido Barzaghi
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the SingleMoleculeFootprinting package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleMoleculeFootprinting.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: SingleMoleculeFootprinting |
Version: 1.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SingleMoleculeFootprinting_1.13.0.tar.gz |
StartedAt: 2024-08-21 09:16:20 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 09:23:47 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 447.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SingleMoleculeFootprinting.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SingleMoleculeFootprinting_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK * this is package ‘SingleMoleculeFootprinting’ version ‘1.13.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘SingleMoleculeFootprinting’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 loading without being on the library search path ... 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 PlotAvgSMF: no visible global function definition for ‘points’ PlotAvgSMF: no visible global function definition for ‘abline’ PlotAvgSMF: no visible global function definition for ‘rect’ PlotAvgSMF: no visible global function definition for ‘text’ PlotSingleMoleculeStack: no visible global function definition for ‘points’ SampleCorrelation: no visible global function definition for ‘pairs’ SampleCorrelation: no visible binding for global variable ‘panel.cor’ SampleCorrelation: no visible binding for global variable ‘panel.hist’ SampleCorrelation: no visible binding for global variable ‘panel.jet’ SingleTFStateQuantificationPlot: no visible global function definition for ‘points’ SingleTFStateQuantificationPlot: no visible global function definition for ‘text’ TFPairStateQuantificationPlot: no visible global function definition for ‘points’ TFPairStateQuantificationPlot: no visible global function definition for ‘text’ Undefined global functions or variables: abline pairs panel.cor panel.hist panel.jet points rect text Consider adding importFrom("graphics", "abline", "pairs", "points", "rect", "text") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’ for details.
SingleMoleculeFootprinting.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SingleMoleculeFootprinting ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘SingleMoleculeFootprinting’ ... ** using staged installation ** 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 (SingleMoleculeFootprinting)
SingleMoleculeFootprinting.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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(SingleMoleculeFootprinting) > > test_check("SingleMoleculeFootprinting") Loading required package: BSgenome 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 object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb 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: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat all necessary alignment files found Detected experiment type: DE all necessary alignment files found see ?SingleMoleculeFootprintingData and browseVignettes('SingleMoleculeFootprintingData') for documentation loading from cache counting alignments...done counting alignments...done Setting QuasR project all necessary alignment files found Calling methylation at all Cytosines 0.9% of reads found with conversion rate above 0.2 Subsetting Cytosines by permissive genomic context (NGCNN, NNCGN) Collapsing strands 0 reads found mapping to the + strand, collapsing to - 0 reads found mapping to the + strand, collapsing to - Filtering Cs for coverage Detected experiment type: DE Subsetting Cytosines by strict genomic context (GCH, HCG) based on the detected experiment type: DE Merging matrixes Collecting summarized methylation for bins Single TF mode [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 34.986 1.815 40.400
SingleMoleculeFootprinting.Rcheck/SingleMoleculeFootprinting-Ex.timings
name | user | system | elapsed | |
BaitCapture | 0.260 | 0.008 | 0.269 | |
BinMethylation | 0.238 | 0.000 | 0.238 | |
CallContextMethylation | 0.223 | 0.016 | 0.240 | |
ConversionRate | 0.226 | 0.024 | 0.251 | |
DetectExperimentType | 0 | 0 | 0 | |
FilterByConversionRate | 0.226 | 0.008 | 0.234 | |
FilterContextCytosines | 0.236 | 0.008 | 0.244 | |
GetQuasRprj | 0.270 | 0.008 | 0.279 | |
GetSingleMolMethMat | 0.244 | 0.004 | 0.249 | |
PlotAvgSMF | 0.238 | 0.000 | 0.238 | |
PlotSM | 0.219 | 0.012 | 0.232 | |
PlotSingleSiteSMF | 0.220 | 0.012 | 0.233 | |
SortReads | 0.226 | 0.004 | 0.231 | |
SortReadsBySingleTF | 0.229 | 0.004 | 0.233 | |
SortReadsByTFCluster | 0.221 | 0.004 | 0.225 | |
StateQuantificationPlot | 0.215 | 0.012 | 0.228 | |