Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:02 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE yamss PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1899/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
yamss 1.14.0 Leslie Myint
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: yamss |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:yamss.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings yamss_1.14.0.tar.gz |
StartedAt: 2020-10-17 06:30:45 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 06:34:47 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 242.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: yamss.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:yamss.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings yamss_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/yamss.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘yamss/DESCRIPTION’ ... OK * this is package ‘yamss’ version ‘1.14.0’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml 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 ‘yamss’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bakedpi 18.307 0.229 12.867 slicepi 12.131 0.079 11.473 CMSraw-class 7.751 0.335 8.561 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.11-bioc/meat/yamss.Rcheck/00check.log’ for details.
yamss.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL yamss ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘yamss’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for request: ‘ifelse’ when loading ‘yamss’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘IRanges’ for request: ‘ifelse’ when loading ‘yamss’ ** testing if installed package can be loaded from final location No methods found in package ‘IRanges’ for request: ‘ifelse’ when loading ‘yamss’ ** testing if installed package keeps a record of temporary installation path * DONE (yamss)
yamss.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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(yamss) 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, which.max, which.min Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum No methods found in package 'IRanges' for request: 'ifelse' when loading 'yamss' > > test_check("yamss") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 36.424 0.770 33.896
yamss.Rcheck/yamss-Ex.timings
name | user | system | elapsed | |
CMSproc-class | 0.007 | 0.001 | 0.007 | |
CMSraw-class | 7.751 | 0.335 | 8.561 | |
CMSslice-class | 0.069 | 0.000 | 0.069 | |
bakedpi | 18.307 | 0.229 | 12.867 | |
diffrep | 0.443 | 0.003 | 0.446 | |
getEICS | 0.101 | 0.000 | 0.038 | |
getTIC | 0.164 | 0.005 | 0.040 | |
plotDensityRegion | 0.009 | 0.000 | 0.008 | |
readMSdata | 1.234 | 0.012 | 1.246 | |
slicepi | 12.131 | 0.079 | 11.473 | |