Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:32:45 -0400 (Tue, 09 Apr 2019).
Package 1588/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
synapter 2.7.1 Laurent Gatto
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: synapter |
Version: 2.7.1 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:synapter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings synapter_2.7.1.tar.gz |
StartedAt: 2019-04-09 03:58:54 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 04:02:38 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 224.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: synapter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:synapter.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings synapter_2.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/synapter.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘synapter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘synapter’ version ‘2.7.1’ * 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 ‘synapter’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Laurent Gatto <[email protected]> [aut, cre] Sebastian Gibb <[email protected]> [aut, cre] * 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 ... NOTE Unexported objects imported by ':::' calls: ‘MSnbase:::.plotSingleSpectrum’ ‘MSnbase:::Spectrum2_mz_sorted’ ‘MSnbase:::commonPeaks’ ‘MSnbase:::numberOfCommonPeaks’ ‘MSnbase:::relaxedMatch’ ‘MSnbase:::utils.list2ssv’ ‘MSnbase:::utils.ssv2list’ ‘MSnbase:::utils.ssv2vec’ ‘MSnbase:::utils.vec2ssv’ See the note in ?`:::` about the use of this operator. * 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 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 Examples with CPU or elapsed time > 5s user system elapsed synergise 14.319 0.493 14.835 Synapter 5.196 0.116 5.329 * 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-3.9-bioc/meat/synapter.Rcheck/00check.log’ for details.
synapter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL synapter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘synapter’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘fragmentmatching.Rmd’ using ‘UTF-8’ ‘synapter.Rmd’ using ‘UTF-8’ ‘synapter2.Rmd’ using ‘UTF-8’ ** 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 (synapter)
synapter.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 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(synapter) Loading required package: MSnbase 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, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min 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")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: ProtGenerics This is MSnbase version 2.9.3 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:stats': smooth The following object is masked from 'package:base': trimws This is the 'synapter' version 2.7.1. Read '?synapter' to get started. > > test_check("synapter") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 78 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 9.762 0.338 10.099
synapter.Rcheck/synapter-Ex.timings
name | user | system | elapsed | |
MasterFdrResults-class | 0 | 0 | 0 | |
Synapter | 5.196 | 0.116 | 5.329 | |
createUniquePeptideDbRds | 0 | 0 | 0 | |
synapterTinyData | 0.227 | 0.012 | 0.238 | |
synergise | 14.319 | 0.493 | 14.835 | |
synergise2 | 0 | 0 | 0 | |