Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:59 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the soGGi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/soGGi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1833/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
soGGi 1.26.0 (landing page) Tom Carroll
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: soGGi |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:soGGi.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings soGGi_1.26.0.tar.gz |
StartedAt: 2022-04-12 09:27:51 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 09:31:56 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 244.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: soGGi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:soGGi.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings soGGi_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/soGGi.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘soGGi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘soGGi’ version ‘1.26.0’ * 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 ‘soGGi’ can be installed ... OK * 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 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 ... NOTE Foreign function call to a different package: .Call("rle_sum_any", ..., PACKAGE = "chipseq") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE plotCuts: warning in ggsave(myP, file = outName): partial argument match of 'file' to 'filename' GetGRanges: no visible global function definition for ‘read.delim’ GetGRanges: possible error in `seqlevels<-`(RegionRanges, force = TRUE, value = `*tmpv*`): unused argument (force = TRUE) findconsensusRegions : <anonymous>: no visible global function definition for ‘weighted.mean’ getShifts: no visible global function definition for ‘readGAlignmentsFromBam’ getSummitScore: no visible global function definition for ‘readGAlignmentsFromBam’ plotHeatmap: no visible global function definition for ‘heat.colors’ plotHeatmap: no visible global function definition for ‘layout’ plotHeatmap: no visible global function definition for ‘par’ plotRegion.ChIPprofile: no visible global function definition for ‘formula’ runFindSummit: no visible global function definition for ‘readGAlignmentsFromBam’ runRegionPlot : <anonymous>: no visible global function definition for ‘spline’ summitPipeline: no visible global function definition for ‘readGAlignmentsFromBam’ plotRegion,ChIPprofile: no visible global function definition for ‘formula’ Undefined global functions or variables: formula heat.colors layout par read.delim readGAlignmentsFromBam spline weighted.mean Consider adding importFrom("grDevices", "heat.colors") importFrom("graphics", "layout", "par") importFrom("stats", "formula", "spline", "weighted.mean") importFrom("utils", "read.delim") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/soGGi.Rcheck/00check.log’ for details.
soGGi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL soGGi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘soGGi’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘soggi.Rnw’ ** 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 (soGGi)
soGGi.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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(soGGi) 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, 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: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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 Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors 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: Biobase 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 > > test_check("soGGi") [ FAIL 0 | WARN 4 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 12.699 0.630 13.312
soGGi.Rcheck/soGGi-Ex.timings
name | user | system | elapsed | |
ChIPprofile | 0.287 | 0.012 | 0.299 | |
Ops | 0.497 | 0.071 | 0.569 | |
groupByOverlaps | 0.431 | 0.008 | 0.439 | |
manipulateObjects | 0.696 | 0.012 | 0.708 | |
normalise | 2.840 | 0.141 | 2.969 | |
normaliseQuantiles | 1.979 | 0.206 | 2.171 | |
orientBy | 0.209 | 0.004 | 0.214 | |
plotRegion | 0.466 | 0.000 | 0.465 | |
pwmToCoverage | 0.002 | 0.000 | 0.002 | |