Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the QuartPAC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QuartPAC.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 1483/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
QuartPAC 1.24.0 (landing page) Gregory Ryslik
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: QuartPAC |
Version: 1.24.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:QuartPAC.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings QuartPAC_1.24.0.tar.gz |
StartedAt: 2021-10-14 11:12:19 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:15:16 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 177.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: QuartPAC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:QuartPAC.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings QuartPAC_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/QuartPAC.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘QuartPAC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘QuartPAC’ version ‘1.24.0’ * 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 ‘QuartPAC’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 alignPositions: no visible global function definition for ‘PhredQuality’ alignPositions: no visible global function definition for ‘pairwiseAlignment’ constructCanonicalNumbering: no visible global function definition for ‘pattern’ constructCanonicalNumbering: no visible global function definition for ‘subject’ constructCanonicalNumbering: no visible global function definition for ‘start’ getMutations : <anonymous>: no visible global function definition for ‘read.table’ getRangeLocInfo: no visible global function definition for ‘aggregate’ quartCluster: no visible global function definition for ‘capture.output’ Undefined global functions or variables: PhredQuality aggregate capture.output pairwiseAlignment pattern read.table start subject Consider adding importFrom("stats", "aggregate", "start") importFrom("utils", "capture.output", "read.table") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed QuartPAC-package 27.721 0.679 32.604 quartCluster 8.331 0.008 12.871 makeAlignedSuperStructure 7.593 0.044 10.226 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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-3.13-bioc/meat/QuartPAC.Rcheck/00check.log’ for details.
QuartPAC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL QuartPAC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘QuartPAC’ ... ** 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 (QuartPAC)
QuartPAC.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > BiocGenerics:::testPackage("QuartPAC") gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith 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 object is masked from 'package:gdata': combine 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:gdata': first, first<- The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:gdata': trim Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'igraph' The following object is masked from 'package:Biostrings': union The following object is masked from 'package:XVector': path The following object is masked from 'package:IRanges': union The following object is masked from 'package:S4Vectors': union The following objects are masked from 'package:BiocGenerics': normalize, path, union The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Attaching package: 'combinat' The following object is masked from 'package:utils': combn Attaching package: 'data.table' The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second The following objects are masked from 'package:gdata': first, last Performing SpacePAC calculations Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 Processing radius # 2 : radius length = 2.00 : Percentage complete 0.50 Performing iPAC Calculations [1] "Running Remapped" Performing GraphPAC Calculations Calculating Remapped Clusters. RUNIT TEST PROTOCOL -- Thu Oct 14 11:15:14 2021 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : QuartPAC RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 25.717 0.865 29.971
QuartPAC.Rcheck/QuartPAC-Ex.timings
name | user | system | elapsed | |
QuartPAC-package | 27.721 | 0.679 | 32.604 | |
getMutations | 0.061 | 0.028 | 1.495 | |
makeAlignedSuperStructure | 7.593 | 0.044 | 10.226 | |
quartCluster | 8.331 | 0.008 | 12.871 | |