Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:53 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the SingleMoleculeFootprinting package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1779/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SingleMoleculeFootprinting 1.0.0 (landing page) Guido Barzaghi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: SingleMoleculeFootprinting |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SingleMoleculeFootprinting_1.0.0.tar.gz |
StartedAt: 2021-10-15 00:05:28 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:12:01 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 392.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SingleMoleculeFootprinting.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SingleMoleculeFootprinting_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SingleMoleculeFootprinting.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK * this is package ‘SingleMoleculeFootprinting’ version ‘1.0.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 R 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 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 in ‘inst/doc’ ... 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-3.13-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’ for details.
SingleMoleculeFootprinting.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SingleMoleculeFootprinting ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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: rtracklayer all necessary alignment files found Detected experiment type: DE all necessary alignment files found snapshotDate(): 2021-05-18 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 1.05% 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 38.130 2.053 41.396
SingleMoleculeFootprinting.Rcheck/SingleMoleculeFootprinting-Ex.timings
name | user | system | elapsed | |
BaitCapture | 0.354 | 0.024 | 0.378 | |
BinMethylation | 0.260 | 0.013 | 0.274 | |
CallContextMethylation | 0.263 | 0.015 | 0.278 | |
ConversionRate | 0.244 | 0.015 | 0.259 | |
DetectExperimentType | 0.001 | 0.000 | 0.001 | |
FilterByConversionRate | 0.297 | 0.016 | 0.313 | |
FilterContextCytosines | 0.306 | 0.018 | 0.324 | |
GetQuasRprj | 0.192 | 0.013 | 0.205 | |
GetSingleMolMethMat | 0.199 | 0.014 | 0.213 | |
PlotAvgSMF | 0.270 | 0.018 | 0.289 | |
PlotSM | 0.263 | 0.014 | 0.278 | |
PlotSingleSiteSMF | 0.275 | 0.014 | 0.290 | |
SortReads | 0.256 | 0.013 | 0.270 | |
SortReadsBySingleTF | 0.254 | 0.012 | 0.265 | |
SortReadsByTFCluster | 0.223 | 0.012 | 0.235 | |
StateQuantificationPlot | 0.247 | 0.011 | 0.259 | |