Genevieve Stein-O'Brien
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/projectR |
| Branch: RELEASE_3_9 |
| Last Commit: 69a67dd |
| Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:17:45 -0400 (Wed, 16 Oct 2019).
| Package 1259/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| projectR 1.0.0 Genevieve Stein-O'Brien
| 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: projectR |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings projectR_1.0.0.tar.gz |
| StartedAt: 2019-10-16 04:06:09 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:09:29 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 199.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: projectR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:projectR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings projectR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/projectR.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘projectR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘projectR’ version ‘1.0.0’ * 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 ... 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 ‘projectR’ 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 * 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-3.9-bioc/meat/projectR.Rcheck/00check.log’ for details.
projectR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL projectR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘projectR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (projectR)
projectR.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-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(projectR)
>
> test_check("projectR")
This is CoGAPS version 3.4.1
Running Standard CoGAPS on 108 genes and 54 samples with parameters:
-- Standard Parameters --
nPatterns 5
nIterations 5000
seed 122
singleCell FALSE
sparseOptimization FALSE
-- Sparsity Parameters --
alpha 0.01
maxGibbsMass 100
Loading Data...Done! (00:00:00)
Running on 1 out of 20 available threads
-- Equilibration Phase --
2500 of 5000, Atoms: 482(225), ChiSq: 28321, Time: 00:00:00 / 00:00:00
5000 of 5000, Atoms: 511(230), ChiSq: 28172, Time: 00:00:02 / 00:00:04
-- Sampling Phase --
2500 of 5000, Atoms: 493(233), ChiSq: 28236, Time: 00:00:03 / 00:00:04
5000 of 5000, Atoms: 491(243), ChiSq: 28317, Time: 00:00:04 / 00:00:04
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 24 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.176 0.590 14.756
projectR.Rcheck/projectR-Ex.timings
| name | user | system | elapsed | |
| auc_mat | 0.044 | 0.004 | 0.048 | |
| cluster2pattern-methods | 0.099 | 0.004 | 0.102 | |
| clusterPlotR-methods | 0 | 0 | 0 | |
| correlateR | 0.095 | 0.000 | 0.096 | |
| geneMatchR | 0.015 | 0.008 | 0.023 | |
| intersectoR-methods | 0.020 | 0.000 | 0.021 | |
| projectR-methods | 4.756 | 0.160 | 4.921 | |
| rotatoR | 0.006 | 0.000 | 0.007 | |