Arne Smits
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/DEP |
| Branch: RELEASE_3_9 |
| Last Commit: 7bd6eed |
| Last Changed Date: 2019-08-06 14:14:37 -0400 (Tue, 06 Aug 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:11:45 -0400 (Wed, 16 Oct 2019).
| Package 416/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEP 1.6.1 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 | |
| Package: DEP |
| Version: 1.6.1 |
| 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_1.6.1.tar.gz |
| StartedAt: 2019-10-16 01:05:04 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:10:28 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 324.5 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_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DEP.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 ‘DEP/DESCRIPTION’ ... OK
* this is package ‘DEP’ version ‘1.6.1’
* 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 8.914 0.004 8.921
plot_dist 5.885 0.003 5.890
* 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 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(DEP)
>
> test_check("DEP")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 333 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
58.884 2.705 63.088
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 2.471 | 0.036 | 2.507 | |
| TMT | 0 | 0 | 0 | |
| add_rejections | 1.179 | 0.008 | 1.188 | |
| analyze_dep | 2.354 | 0.043 | 2.403 | |
| filter_missval | 0.344 | 0.004 | 0.348 | |
| filter_proteins | 0.225 | 0.000 | 0.224 | |
| get_df_long | 0.802 | 0.000 | 0.801 | |
| get_df_wide | 1.146 | 0.004 | 1.149 | |
| get_prefix | 0.004 | 0.000 | 0.005 | |
| get_results | 1.355 | 0.004 | 1.360 | |
| get_suffix | 0.001 | 0.000 | 0.002 | |
| import_IsobarQuant | 0 | 0 | 0 | |
| import_MaxQuant | 0.082 | 0.000 | 0.082 | |
| impute | 1.176 | 0.004 | 1.180 | |
| make_se | 0.03 | 0.00 | 0.03 | |
| make_se_parse | 0.07 | 0.00 | 0.07 | |
| make_unique | 0.014 | 0.000 | 0.014 | |
| manual_impute | 0.542 | 0.003 | 0.546 | |
| meanSdPlot | 0.517 | 0.004 | 0.521 | |
| normalize_vsn | 0.288 | 0.004 | 0.292 | |
| plot_all | 1.332 | 0.004 | 1.336 | |
| plot_cond | 1.819 | 0.020 | 1.839 | |
| plot_cond_freq | 1.433 | 0.004 | 1.437 | |
| plot_cond_overlap | 1.433 | 0.004 | 1.437 | |
| plot_cor | 1.426 | 0.000 | 1.426 | |
| plot_coverage | 0.825 | 0.000 | 0.825 | |
| plot_detect | 1.097 | 0.020 | 1.116 | |
| plot_dist | 5.885 | 0.003 | 5.890 | |
| plot_frequency | 0.583 | 0.004 | 0.587 | |
| plot_gsea | 1.182 | 0.011 | 1.194 | |
| plot_heatmap | 4.303 | 0.019 | 4.578 | |
| plot_imputation | 2.414 | 0.000 | 2.413 | |
| plot_missval | 1.049 | 0.024 | 1.073 | |
| plot_normalization | 1.225 | 0.004 | 1.229 | |
| plot_numbers | 0.421 | 0.000 | 0.421 | |
| plot_p_hist | 1.352 | 0.000 | 1.351 | |
| plot_pca | 1.440 | 0.004 | 1.444 | |
| plot_single | 2.109 | 0.008 | 2.117 | |
| plot_volcano | 8.914 | 0.004 | 8.921 | |
| process | 1.903 | 0.004 | 1.908 | |
| report | 0.000 | 0.000 | 0.001 | |
| run_app | 0.000 | 0.000 | 0.001 | |
| se2msn | 0.150 | 0.004 | 0.155 | |
| test_diff | 1.441 | 0.000 | 1.441 | |
| test_gsea | 1.142 | 0.008 | 1.151 | |
| theme_DEP1 | 0.475 | 0.000 | 0.475 | |
| theme_DEP2 | 0.431 | 0.000 | 0.431 | |