Arne Smits
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DEP |
| Branch: master |
| Last Commit: ed8e222 |
| Last Changed Date: 2019-03-11 12:11:27 -0400 (Mon, 11 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:48:39 -0400 (Tue, 09 Apr 2019).
| Package 409/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEP 1.5.3 Arne Smits
| 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: DEP |
| Version: 1.5.3 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEP_1.5.3.tar.gz |
| StartedAt: 2019-04-08 23:58:33 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-09 00:03:51 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 317.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DEP_1.5.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DEP.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 ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.5.3’
* 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 ‘DEP’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_volcano 7.775 0 7.794
* 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: OK
DEP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘DEP’ ... ** 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 (DEP)
DEP.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(DEP)
>
> test_check("DEP")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 334 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
48.418 2.575 54.629
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 3.080 | 0.015 | 3.098 | |
| TMT | 0 | 0 | 0 | |
| add_rejections | 1.178 | 0.028 | 1.206 | |
| analyze_dep | 1.787 | 0.036 | 1.823 | |
| filter_missval | 0.437 | 0.000 | 0.437 | |
| filter_proteins | 0.267 | 0.004 | 0.271 | |
| get_df_long | 0.776 | 0.000 | 0.776 | |
| get_df_wide | 1.286 | 0.000 | 1.286 | |
| get_prefix | 0.002 | 0.000 | 0.002 | |
| get_results | 1.394 | 0.000 | 1.394 | |
| get_suffix | 0.001 | 0.000 | 0.001 | |
| import_IsobarQuant | 0 | 0 | 0 | |
| import_MaxQuant | 0.038 | 0.000 | 0.038 | |
| impute | 1.550 | 0.012 | 1.562 | |
| make_se | 0.055 | 0.004 | 0.059 | |
| make_se_parse | 0.106 | 0.004 | 0.110 | |
| make_unique | 0.027 | 0.000 | 0.027 | |
| manual_impute | 0.987 | 0.000 | 0.987 | |
| meanSdPlot | 0.970 | 0.008 | 0.978 | |
| normalize_vsn | 0.549 | 0.000 | 0.548 | |
| plot_all | 2.359 | 0.020 | 2.379 | |
| plot_cond | 2.585 | 0.012 | 2.598 | |
| plot_cond_freq | 1.362 | 0.008 | 1.370 | |
| plot_cond_overlap | 0.999 | 0.008 | 1.007 | |
| plot_cor | 1.468 | 0.000 | 1.467 | |
| plot_coverage | 0.574 | 0.000 | 0.575 | |
| plot_detect | 0.692 | 0.004 | 0.697 | |
| plot_dist | 4.131 | 0.004 | 4.135 | |
| plot_frequency | 0.622 | 0.000 | 0.622 | |
| plot_gsea | 1.228 | 0.004 | 1.232 | |
| plot_heatmap | 3.280 | 0.008 | 3.288 | |
| plot_imputation | 1.982 | 0.012 | 1.994 | |
| plot_missval | 2.129 | 0.000 | 2.129 | |
| plot_normalization | 2.816 | 0.012 | 2.830 | |
| plot_numbers | 0.773 | 0.000 | 0.773 | |
| plot_p_hist | 1.638 | 0.000 | 1.638 | |
| plot_pca | 1.587 | 0.000 | 1.600 | |
| plot_single | 1.821 | 0.000 | 1.833 | |
| plot_volcano | 7.775 | 0.000 | 7.794 | |
| process | 1.362 | 0.000 | 1.366 | |
| report | 0 | 0 | 0 | |
| run_app | 0.001 | 0.000 | 0.001 | |
| se2msn | 0.093 | 0.000 | 0.093 | |
| test_diff | 0.977 | 0.004 | 0.981 | |
| test_gsea | 0.774 | 0.004 | 0.778 | |
| theme_DEP1 | 0.395 | 0.000 | 0.395 | |
| theme_DEP2 | 0.458 | 0.000 | 0.458 | |