Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -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 1978/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SingleMoleculeFootprinting 2.0.0 (landing page) Guido Barzaghi
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | 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. |
Package: SingleMoleculeFootprinting |
Version: 2.0.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SingleMoleculeFootprinting_2.0.0.tar.gz |
StartedAt: 2024-12-20 09:48:32 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 10:00:30 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 717.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SingleMoleculeFootprinting.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SingleMoleculeFootprinting_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK * this is package ‘SingleMoleculeFootprinting’ version ‘2.0.0’ * 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 ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biostrings::setequal’ by ‘dplyr::setequal’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Biostrings::collapse’ by ‘dplyr::collapse’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Matrix::image’ by ‘graphics::image’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::between’ by ‘plyranges::between’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n_distinct’ by ‘plyranges::n_distinct’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n’ by ‘plyranges::n’ when loading ‘SingleMoleculeFootprinting’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck/00install.out’ for details. * 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 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 Create_MethylationCallingWindows: no visible binding for global variable ‘idx’ GRanges_to_DF: no visible binding for global variable ‘Sample’ GRanges_to_DF: no visible binding for global variable ‘Score’ LowCoverageMethRate_RMSE: no visible binding for global variable ‘Sample’ PlotAvgSMF: no visible binding for global variable ‘MethRate’ PlotSingleMoleculeStack : <anonymous>: no visible binding for global variable ‘Coordinate’ PlotSingleMoleculeStack : <anonymous>: no visible binding for global variable ‘Methylation’ PlotSingleMoleculeStack: no visible binding for global variable ‘Sample’ StateQuantificationPlot: no visible binding for global variable ‘State’ StateQuantificationPlot: no visible binding for global variable ‘Pattern’ StateQuantificationPlot: no visible binding for global variable ‘Bin’ StateQuantificationPlot: no visible binding for global variable ‘Methylation’ Undefined global functions or variables: Bin Coordinate MethRate Methylation Pattern Sample Score State idx * 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 ... NOTE S3 methods shown with full name in Rd file 'cbind.fill.Matrix.Rd': ‘cbind.fill.Matrix’ S3 methods shown with full name in Rd file 'rbind.fill.Matrix.Rd': ‘rbind.fill.Matrix’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GetSingleMolMethMat 6.757 1.941 8.949 * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’ for details.
SingleMoleculeFootprinting.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleMoleculeFootprinting ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SingleMoleculeFootprinting’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biostrings::setequal’ by ‘dplyr::setequal’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Biostrings::collapse’ by ‘dplyr::collapse’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Matrix::image’ by ‘graphics::image’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::between’ by ‘plyranges::between’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n_distinct’ by ‘plyranges::n_distinct’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n’ by ‘plyranges::n’ when loading ‘SingleMoleculeFootprinting’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biostrings::setequal’ by ‘dplyr::setequal’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Biostrings::collapse’ by ‘dplyr::collapse’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Matrix::image’ by ‘graphics::image’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::between’ by ‘plyranges::between’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n_distinct’ by ‘plyranges::n_distinct’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n’ by ‘plyranges::n’ when loading ‘SingleMoleculeFootprinting’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biostrings::setequal’ by ‘dplyr::setequal’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Biostrings::collapse’ by ‘dplyr::collapse’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘Matrix::image’ by ‘graphics::image’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::between’ by ‘plyranges::between’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n_distinct’ by ‘plyranges::n_distinct’ when loading ‘SingleMoleculeFootprinting’ Warning: replacing previous import ‘dplyr::n’ by ‘plyranges::n’ when loading ‘SingleMoleculeFootprinting’ ** testing if installed package keeps a record of temporary installation path * DONE (SingleMoleculeFootprinting)
SingleMoleculeFootprinting.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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(SingleMoleculeFootprinting) There were 12 warnings (use warnings() to see them) > > 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, saveRDS, 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 all necessary alignment files found 5334 reads found mapping to the - strand, collapsing to + 5334 reads found mapping to the - strand, collapsing to + Detected experiment type: DE Collecting summarized methylation for bins Subsetting those reads that cover all bins Summarizing reads into patterns Splitting reads by pattern [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ] > > proc.time() user system elapsed 51.929 3.924 57.308
SingleMoleculeFootprinting.Rcheck/SingleMoleculeFootprinting-Ex.timings
name | user | system | elapsed | |
Arrange_TFBSs_clusters | 0.973 | 0.028 | 1.020 | |
BaitCapture | 0.001 | 0.000 | 0.001 | |
BinMethylation | 0.435 | 0.022 | 0.464 | |
CallContextMethylation | 0.001 | 0.001 | 0.002 | |
CollapseStrands | 0 | 0 | 0 | |
CollapseStrandsSM | 0.000 | 0.001 | 0.000 | |
CollectCompositeData | 0.001 | 0.001 | 0.002 | |
CompositeMethylationCorrelation | 0.001 | 0.001 | 0.001 | |
CompositePlot | 0.000 | 0.001 | 0.000 | |
ConversionRate | 0 | 0 | 0 | |
Create_MethylationCallingWindows | 0.152 | 0.002 | 0.156 | |
DetectExperimentType | 1.150 | 0.150 | 1.341 | |
FilterByConversionRate | 1.048 | 0.397 | 1.462 | |
FilterContextCytosines | 0.850 | 0.035 | 0.908 | |
GetQuasRprj | 2.867 | 1.146 | 4.225 | |
GetSingleMolMethMat | 6.757 | 1.941 | 8.949 | |
MaskSNPs | 0.267 | 0.003 | 0.272 | |
PlotAvgSMF | 1.198 | 0.033 | 1.433 | |
PlotSM | 1.936 | 0.115 | 2.284 | |
PlotSingleMoleculeStack | 1.904 | 0.224 | 2.168 | |
PlotSingleSiteSMF | 3.545 | 0.248 | 4.013 | |
SingleTFStates | 0.005 | 0.001 | 0.006 | |
SortReads | 0.164 | 0.010 | 0.377 | |
SortReadsBySingleTF | 0.050 | 0.004 | 0.054 | |
SortReadsBySingleTF_MultiSiteWrapper | 0.001 | 0.000 | 0.002 | |
SortReadsByTFCluster | 0.052 | 0.003 | 0.055 | |
SortReadsByTFCluster_MultiSiteWrapper | 0.001 | 0.001 | 0.002 | |
StateQuantification | 0.131 | 0.005 | 0.138 | |
StateQuantificationBySingleTF | 0.093 | 0.003 | 0.097 | |
StateQuantificationByTFPair | 0.099 | 0.002 | 0.101 | |
StateQuantificationPlot | 0.820 | 0.064 | 0.970 | |
TFPairStates | 0.018 | 0.002 | 0.022 | |
cbind.fill.Matrix | 0.960 | 1.422 | 2.505 | |
rbind.fill.Matrix | 0.971 | 1.433 | 2.450 | |