Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 13:02:04 -0400 (Wed, 16 Oct 2019).
Package 1201/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
phantasus 1.4.0 Alexey Sergushichev
| 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 |
Package: phantasus |
Version: 1.4.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phantasus_1.4.0.tar.gz |
StartedAt: 2019-10-16 05:30:38 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 05:36:14 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 335.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: phantasus.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phantasus_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/phantasus.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘phantasus/DESCRIPTION’ ... OK * this is package ‘phantasus’ version ‘1.4.0’ * 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 ‘phantasus’ can be installed ... OK * checking installed package size ... NOTE installed size is 27.4Mb sub-directories of 1Mb or more: testdata 4.1Mb www 23.0Mb * checking package 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 ... NOTE Unexported objects imported by ':::' calls: 'GEOquery:::getDirListing' 'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac' 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 ... NOTE loadSession: no visible binding for global variable 'es' Undefined global functions or variables: es * checking Rd files ... NOTE prepare_Rd: convertByAnnotationDB.Rd:27-32: Dropping empty section \examples * 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 or elapsed time > 5s user system elapsed getGSE 8.495 1.117 10.404 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/phantasus.Rcheck/00check.log’ for details.
phantasus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phantasus ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘phantasus’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (phantasus)
phantasus.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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(phantasus) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading config from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/opencpu/config/defaults.conf Loading config from /Users/biocbuild/Library/Application Support/opencpu/user.conf > > test_check("phantasus") trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53986/matrix/GSE53986_series_matrix.txt.gz' Content type 'application/x-gzip' length 2848655 bytes (2.7 MB) ================================================== downloaded 2.7 MB trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz' trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6103_series_matrix.txt.gz' Content type 'application/x-gzip' length 596707 bytes (582 KB) ================================================== downloaded 582 KB trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6885_series_matrix.txt.gz' Content type 'application/x-gzip' length 1273889 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz' Content type 'application/x-gzip' length 1807552 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz' Content type 'application/x-gzip' length 1250109 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz' ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 94 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ] > > proc.time() user system elapsed 110.411 12.392 131.517
phantasus.Rcheck/phantasus-Ex.timings
name | user | system | elapsed | |
adjustDataset | 0 | 0 | 0 | |
annotationDBMeta | 0.001 | 0.000 | 0.000 | |
calcPCA | 0.000 | 0.000 | 0.001 | |
checkGPLs | 0.001 | 0.000 | 0.000 | |
collapseDataset | 0.000 | 0.000 | 0.001 | |
createES | 0 | 0 | 0 | |
es | 0.000 | 0.000 | 0.001 | |
getES | 1.280 | 0.127 | 1.775 | |
getGDS | 1.267 | 0.069 | 1.339 | |
getGSE | 8.495 | 1.117 | 10.404 | |
limmaAnalysis | 0.000 | 0.001 | 0.001 | |
loadGEO | 0.000 | 0.000 | 0.001 | |
performKmeans | 0.001 | 0.000 | 0.000 | |
queryAnnotationDBMeta | 0.001 | 0.000 | 0.000 | |
read.gct | 0.045 | 0.001 | 0.048 | |
reparseCachedESs | 1.587 | 0.112 | 1.701 | |
servePhantasus | 0.001 | 0.000 | 0.000 | |
write.gct | 0.047 | 0.001 | 0.047 | |