Arne Smits
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DEP |
| Branch: RELEASE_3_7 |
| Last Commit: b722d2e |
| Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:33 -0400 (Wed, 17 Oct 2018).
| Package 369/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEP 1.2.0 Arne Smits
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DEP |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DEP_1.2.0.tar.gz |
| StartedAt: 2018-10-15 23:45:52 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:50:20 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 268.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DEP.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DEP_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/DEP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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 7.2 0.004 7.21
* 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-3.7-bioc/R/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘DEP’ ... ** 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 * DONE (DEP)
DEP.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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: 327 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
45.160 2.228 48.272
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 1.940 | 0.044 | 1.985 | |
| TMT | 0.000 | 0.000 | 0.001 | |
| add_rejections | 1.068 | 0.044 | 1.110 | |
| analyze_dep | 2.100 | 0.024 | 2.129 | |
| filter_missval | 0.824 | 0.000 | 0.822 | |
| filter_proteins | 0.456 | 0.000 | 0.457 | |
| get_df_long | 1.080 | 0.000 | 1.079 | |
| get_df_wide | 1.508 | 0.000 | 1.510 | |
| get_prefix | 0.000 | 0.000 | 0.002 | |
| get_results | 1.208 | 0.000 | 1.211 | |
| get_suffix | 0.000 | 0.000 | 0.001 | |
| import_IsobarQuant | 0.000 | 0.000 | 0.001 | |
| import_MaxQuant | 0.040 | 0.004 | 0.047 | |
| impute | 1.448 | 0.000 | 1.450 | |
| make_se | 0.044 | 0.000 | 0.045 | |
| make_se_parse | 0.064 | 0.000 | 0.065 | |
| make_unique | 0.020 | 0.000 | 0.018 | |
| manual_impute | 0.848 | 0.000 | 0.849 | |
| meanSdPlot | 0.884 | 0.004 | 0.885 | |
| normalize_vsn | 0.576 | 0.000 | 0.575 | |
| plot_all | 1.872 | 0.008 | 1.883 | |
| plot_cond | 1.436 | 0.008 | 1.443 | |
| plot_cond_freq | 1.240 | 0.000 | 1.243 | |
| plot_cond_overlap | 1.212 | 0.000 | 1.214 | |
| plot_cor | 1.612 | 0.004 | 1.615 | |
| plot_coverage | 0.792 | 0.000 | 0.794 | |
| plot_detect | 1.064 | 0.000 | 1.062 | |
| plot_dist | 2.632 | 0.000 | 2.634 | |
| plot_frequency | 0.644 | 0.000 | 0.645 | |
| plot_gsea | 1.096 | 0.000 | 1.098 | |
| plot_heatmap | 4.232 | 0.004 | 4.240 | |
| plot_imputation | 1.812 | 0.016 | 1.828 | |
| plot_missval | 2.236 | 0.020 | 2.256 | |
| plot_normalization | 1.744 | 0.020 | 1.767 | |
| plot_numbers | 0.700 | 0.000 | 0.701 | |
| plot_p_hist | 1.700 | 0.000 | 1.704 | |
| plot_pca | 1.840 | 0.000 | 1.839 | |
| plot_single | 2.020 | 0.004 | 2.027 | |
| plot_volcano | 7.200 | 0.004 | 7.210 | |
| process | 1.62 | 0.00 | 1.62 | |
| report | 0 | 0 | 0 | |
| run_app | 0.000 | 0.000 | 0.001 | |
| se2msn | 0.108 | 0.000 | 0.110 | |
| test_diff | 1.436 | 0.000 | 1.435 | |
| test_gsea | 0.952 | 0.000 | 0.951 | |
| theme_DEP1 | 0.704 | 0.000 | 0.706 | |
| theme_DEP2 | 0.760 | 0.000 | 0.759 | |