Arne Smits
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/DEP |
| Branch: RELEASE_3_10 |
| Last Commit: 086f5d1 |
| Last Changed Date: 2019-10-29 13:10:39 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:13:03 -0400 (Wed, 15 Apr 2020).
| Package 436/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEP 1.8.0 Arne Smits
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DEP |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DEP_1.8.0.tar.gz |
| StartedAt: 2020-04-15 05:01:56 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:08:09 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 372.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DEP_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/DEP.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 ‘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 9.220 0.008 9.253
plot_dist 5.432 0.004 5.546
* 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-3.10-bioc/R/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(DEP)
>
> test_check("DEP")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 333 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
>
> proc.time()
user system elapsed
63.480 2.712 71.395
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 2.264 | 0.036 | 2.349 | |
| TMT | 0 | 0 | 0 | |
| add_rejections | 1.160 | 0.004 | 1.235 | |
| analyze_dep | 2.772 | 0.028 | 2.811 | |
| filter_missval | 0.564 | 0.000 | 0.564 | |
| filter_proteins | 0.360 | 0.000 | 0.379 | |
| get_df_long | 1.220 | 0.000 | 1.235 | |
| get_df_wide | 1.708 | 0.012 | 1.720 | |
| get_prefix | 0.004 | 0.000 | 0.003 | |
| get_results | 1.136 | 0.016 | 1.153 | |
| get_suffix | 0.000 | 0.000 | 0.001 | |
| import_IsobarQuant | 0 | 0 | 0 | |
| import_MaxQuant | 0.056 | 0.000 | 0.057 | |
| impute | 1.680 | 0.036 | 1.747 | |
| make_se | 0.048 | 0.020 | 0.067 | |
| make_se_parse | 0.100 | 0.004 | 0.103 | |
| make_unique | 0.028 | 0.000 | 0.028 | |
| manual_impute | 1.508 | 0.000 | 1.508 | |
| meanSdPlot | 0.756 | 0.000 | 0.758 | |
| normalize_vsn | 0.380 | 0.012 | 0.392 | |
| plot_all | 1.996 | 0.028 | 2.026 | |
| plot_cond | 1.800 | 0.012 | 1.838 | |
| plot_cond_freq | 1.392 | 0.000 | 1.395 | |
| plot_cond_overlap | 1.412 | 0.000 | 1.414 | |
| plot_cor | 1.704 | 0.000 | 1.722 | |
| plot_coverage | 0.808 | 0.004 | 0.824 | |
| plot_detect | 1.128 | 0.008 | 1.148 | |
| plot_dist | 5.432 | 0.004 | 5.546 | |
| plot_frequency | 0.488 | 0.000 | 0.488 | |
| plot_gsea | 1.632 | 0.000 | 1.649 | |
| plot_heatmap | 4.268 | 0.012 | 4.371 | |
| plot_imputation | 1.952 | 0.012 | 1.979 | |
| plot_missval | 1.992 | 0.000 | 2.000 | |
| plot_normalization | 1.980 | 0.016 | 2.004 | |
| plot_numbers | 0.688 | 0.000 | 0.692 | |
| plot_p_hist | 2.340 | 0.008 | 2.355 | |
| plot_pca | 2.040 | 0.004 | 2.078 | |
| plot_single | 2.636 | 0.008 | 2.658 | |
| plot_volcano | 9.220 | 0.008 | 9.253 | |
| process | 1.628 | 0.000 | 1.634 | |
| report | 0 | 0 | 0 | |
| run_app | 0 | 0 | 0 | |
| se2msn | 0.120 | 0.000 | 0.123 | |
| test_diff | 2.100 | 0.000 | 2.109 | |
| test_gsea | 1.056 | 0.008 | 1.070 | |
| theme_DEP1 | 0.508 | 0.000 | 0.510 | |
| theme_DEP2 | 0.644 | 0.000 | 0.649 | |