Arne Smits
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/DEP |
| Branch: RELEASE_3_6 |
| Last Commit: 471c4fa |
| Last Changed Date: 2017-11-17 03:14:10 -0400 (Fri, 17 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:16:33 -0400 (Thu, 12 Apr 2018).
| Package 352/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEP 1.0.1 Arne Smits
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: DEP |
| Version: 1.0.1 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DEP_1.0.1.tar.gz |
| StartedAt: 2018-04-11 22:50:49 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:55:14 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 265.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEP.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DEP_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DEP.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.1’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_heatmap 7.788 0.020 7.832
plot_volcano 6.320 0.012 6.336
LFQ 4.948 0.068 5.679
* 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
* installing *source* package ‘DEP’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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")
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
══ testthat results ═══════════════════════════════════════════════════════════
OK: 290 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
53.664 1.608 56.142
DEP.Rcheck/DEP-Ex.timings
| name | user | system | elapsed | |
| LFQ | 4.948 | 0.068 | 5.679 | |
| TMT | 0.000 | 0.000 | 0.001 | |
| add_rejections | 2.840 | 0.004 | 2.849 | |
| analyze_dep | 4.328 | 0.040 | 4.384 | |
| filter_missval | 0.892 | 0.028 | 0.923 | |
| get_df_long | 1.164 | 0.004 | 1.171 | |
| get_df_wide | 1.008 | 0.004 | 1.013 | |
| get_prefix | 0.004 | 0.000 | 0.006 | |
| get_results | 1.224 | 0.000 | 1.226 | |
| import_IsobarQuant | 0 | 0 | 0 | |
| import_MaxQuant | 0.080 | 0.000 | 0.078 | |
| impute | 1.276 | 0.000 | 1.277 | |
| make_se | 0.044 | 0.000 | 0.047 | |
| make_se_parse | 0.096 | 0.000 | 0.095 | |
| make_unique | 0.020 | 0.000 | 0.023 | |
| manual_impute | 0.892 | 0.004 | 0.900 | |
| meanSdPlot | 1.616 | 0.008 | 1.675 | |
| normalize_vsn | 0.536 | 0.000 | 0.538 | |
| plot_all | 2.072 | 0.000 | 2.070 | |
| plot_cond | 1.62 | 0.00 | 1.64 | |
| plot_cond_freq | 1.736 | 0.000 | 1.737 | |
| plot_cond_overlap | 1.928 | 0.008 | 1.940 | |
| plot_cor | 2.248 | 0.000 | 2.248 | |
| plot_coverage | 0.680 | 0.000 | 0.679 | |
| plot_detect | 1.188 | 0.000 | 1.186 | |
| plot_frequency | 0.704 | 0.000 | 0.707 | |
| plot_gsea | 1.184 | 0.008 | 1.191 | |
| plot_heatmap | 7.788 | 0.020 | 7.832 | |
| plot_imputation | 1.452 | 0.008 | 1.462 | |
| plot_missval | 2.408 | 0.004 | 2.412 | |
| plot_normalization | 1.348 | 0.012 | 1.361 | |
| plot_numbers | 1.084 | 0.000 | 1.083 | |
| plot_p_hist | 1.768 | 0.008 | 1.779 | |
| plot_pca | 1.620 | 0.008 | 1.627 | |
| plot_single | 2.388 | 0.000 | 2.389 | |
| plot_volcano | 6.320 | 0.012 | 6.336 | |
| process | 1.492 | 0.008 | 1.501 | |
| report | 0 | 0 | 0 | |
| run_app | 0 | 0 | 0 | |
| se2msn | 0.084 | 0.000 | 0.085 | |
| test_diff | 1.288 | 0.000 | 1.291 | |
| test_gsea | 1.748 | 0.004 | 1.754 | |
| theme_DEP1 | 0.636 | 0.000 | 0.637 | |
| theme_DEP2 | 0.720 | 0.000 | 0.723 | |