Arne Smits
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DEP |
| Branch: RELEASE_3_8 |
| Last Commit: e024011 |
| Last Changed Date: 2019-01-04 13:28:37 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:53 -0400 (Tue, 16 Apr 2019).
| Package 392/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEP 1.4.1 Arne Smits
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: DEP |
| Version: 1.4.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEP_1.4.1.tar.gz |
| StartedAt: 2019-04-15 23:26:24 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:32:19 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 354.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEP_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DEP.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.4.1’
* 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 7.464 0.050 7.581
plot_heatmap 5.934 0.062 6.065
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DEP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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 3.5.3 (2019-03-11) -- "Great Truth"
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(DEP)
>
> test_check("DEP")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 327 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
67.779 2.048 70.718
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 2.350 | 0.079 | 2.465 | |
| TMT | 0 | 0 | 0 | |
| add_rejections | 1.615 | 0.096 | 1.726 | |
| analyze_dep | 3.067 | 0.157 | 3.275 | |
| filter_missval | 0.990 | 0.060 | 1.059 | |
| filter_proteins | 0.490 | 0.028 | 0.524 | |
| get_df_long | 1.841 | 0.043 | 1.897 | |
| get_df_wide | 1.257 | 0.049 | 1.320 | |
| get_prefix | 0.003 | 0.000 | 0.003 | |
| get_results | 1.473 | 0.051 | 1.538 | |
| get_suffix | 0.002 | 0.000 | 0.002 | |
| import_IsobarQuant | 0.000 | 0.001 | 0.001 | |
| import_MaxQuant | 0.056 | 0.002 | 0.059 | |
| impute | 2.110 | 0.057 | 2.194 | |
| make_se | 0.040 | 0.001 | 0.042 | |
| make_se_parse | 0.115 | 0.006 | 0.125 | |
| make_unique | 0.032 | 0.001 | 0.032 | |
| manual_impute | 1.005 | 0.046 | 1.056 | |
| meanSdPlot | 0.984 | 0.026 | 1.015 | |
| normalize_vsn | 0.597 | 0.025 | 0.632 | |
| plot_all | 2.392 | 0.088 | 2.508 | |
| plot_cond | 1.885 | 0.056 | 1.962 | |
| plot_cond_freq | 1.644 | 0.045 | 1.707 | |
| plot_cond_overlap | 1.637 | 0.039 | 1.706 | |
| plot_cor | 2.036 | 0.035 | 2.085 | |
| plot_coverage | 0.985 | 0.029 | 1.031 | |
| plot_detect | 1.191 | 0.029 | 1.235 | |
| plot_dist | 3.716 | 0.061 | 3.820 | |
| plot_frequency | 0.692 | 0.027 | 0.727 | |
| plot_gsea | 1.331 | 0.047 | 1.400 | |
| plot_heatmap | 5.934 | 0.062 | 6.065 | |
| plot_imputation | 2.756 | 0.100 | 2.898 | |
| plot_missval | 2.395 | 0.103 | 2.509 | |
| plot_normalization | 2.374 | 0.093 | 2.486 | |
| plot_numbers | 0.863 | 0.019 | 0.888 | |
| plot_p_hist | 2.144 | 0.036 | 2.200 | |
| plot_pca | 2.224 | 0.043 | 2.281 | |
| plot_single | 2.288 | 0.036 | 2.337 | |
| plot_volcano | 7.464 | 0.050 | 7.581 | |
| process | 2.396 | 0.074 | 2.505 | |
| report | 0 | 0 | 0 | |
| run_app | 0 | 0 | 0 | |
| se2msn | 0.175 | 0.002 | 0.177 | |
| test_diff | 1.734 | 0.060 | 1.810 | |
| test_gsea | 1.484 | 0.042 | 1.539 | |
| theme_DEP1 | 0.670 | 0.022 | 0.702 | |
| theme_DEP2 | 0.877 | 0.023 | 0.911 | |