Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:39 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1949/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SeqSQC 1.26.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | 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 | NA | |||||||||
To the developers/maintainers of the SeqSQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqSQC.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: SeqSQC |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SeqSQC_1.26.0.tar.gz |
StartedAt: 2024-08-12 03:43:45 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 03:47:02 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 197.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SeqSQC.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SeqSQC.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SeqSQC_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SeqSQC.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘SeqSQC/DESCRIPTION’ ... OK * this is package ‘SeqSQC’ version ‘1.26.0’ * 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 ‘SeqSQC’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘S4Vectors::rename’ by ‘plotly::rename’ when loading ‘SeqSQC’ Warning: replacing previous import ‘IRanges::slice’ by ‘plotly::slice’ when loading ‘SeqSQC’ Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘SeqSQC’ See ‘/home/biocbuild/bbs-3.19-bioc/meat/SeqSQC.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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Load benchmark data from ExperimentHub Cannot process chunk/lines: o added in the R script, will download only once with first time running of the LoadVfile() or sampleQC(). Cannot process chunk/lines: Bioconductor submission check: Cannot process chunk/lines: o Added unit test. Cannot process chunk/lines: o Added a NEWS file to keep track of changes Cannot process chunk/lines: o Added zzz.R to fix the no visible binding for global functions or variables. Cannot process chunk/lines: o Added the "example_sub.vcf" for 1000 lines of variants to run as example in the package vignette. Cannot process chunk/lines: o Added accessor methods for SeqSQCclass data structure to get the slots of "gdsfile" and "QCresult". Cannot process chunk/lines: Vignettes: Cannot process chunk/lines: o Added bioconductor installation and library load section in the vignette. Cannot process chunk/lines: o Added runnable example vcf file added in "inst/extdata/example_sub.vcf", with 1000 lines of variants. Cannot process chunk/lines: MAN: Cannot process chunk/lines: o added package documentation for dataset, class, methods and constructor. * 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 whether startup messages can be suppressed ... 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 ... OK * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed LoadVfile 15.067 2.127 17.746 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/SeqSQC.Rcheck/00check.log’ for details.
SeqSQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SeqSQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SeqSQC’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘S4Vectors::rename’ by ‘plotly::rename’ when loading ‘SeqSQC’ Warning: replacing previous import ‘IRanges::slice’ by ‘plotly::slice’ when loading ‘SeqSQC’ Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘SeqSQC’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘S4Vectors::rename’ by ‘plotly::rename’ when loading ‘SeqSQC’ Warning: replacing previous import ‘IRanges::slice’ by ‘plotly::slice’ when loading ‘SeqSQC’ Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘SeqSQC’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘S4Vectors::rename’ by ‘plotly::rename’ when loading ‘SeqSQC’ Warning: replacing previous import ‘IRanges::slice’ by ‘plotly::slice’ when loading ‘SeqSQC’ Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘SeqSQC’ ** testing if installed package keeps a record of temporary installation path * DONE (SeqSQC)
SeqSQC.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: x86_64-pc-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(SeqSQC) Loading required package: ExperimentHub 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: AnnotationHub Loading required package: BiocFileCache Loading required package: dbplyr Loading required package: SNPRelate Loading required package: gdsfmt SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2) Warning messages: 1: replacing previous import 'S4Vectors::rename' by 'plotly::rename' when loading 'SeqSQC' 2: replacing previous import 'IRanges::slice' by 'plotly::slice' when loading 'SeqSQC' 3: replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot' when loading 'SeqSQC' > > test_check("SeqSQC") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 5.402 0.297 5.691
SeqSQC.Rcheck/SeqSQC-Ex.timings
name | user | system | elapsed | |
IBDCheck | 0.493 | 0.031 | 0.528 | |
IBDRemove | 0.420 | 0.032 | 0.453 | |
Inbreeding | 4.628 | 0.148 | 4.776 | |
LoadVfile | 15.067 | 2.127 | 17.746 | |
MissingRate | 0.309 | 0.068 | 0.377 | |
PCACheck | 0.499 | 0.028 | 0.527 | |
RenderReport | 2.680 | 0.154 | 2.843 | |
SeqOpen | 0.032 | 0.000 | 0.032 | |
SeqSQC-class | 0.010 | 0.000 | 0.009 | |
SexCheck | 0.341 | 0.008 | 0.350 | |
plotQC | 0.173 | 0.003 | 0.177 | |
problemList | 0.012 | 0.000 | 0.012 | |
sampleQC | 0 | 0 | 0 | |