Multiple platform build/check report for BioC 3.9 - CHECK report for DEP on tokay2

Package: DEP

Version: 1.6.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEP_1.6.1.tar.gz

StartedAt: 2019-10-16 03:09:51 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:17:26 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 454.4 seconds

RetCode: 0

Status: OK

CheckDir: DEP.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEP_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEP.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_volcano 5.79   0.03    5.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_volcano 5.09   0.03    5.13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DEP_1.6.1.tar.gz && rm -rf DEP.buildbin-libdir && mkdir DEP.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEP.buildbin-libdir DEP_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DEP_1.6.1.zip && rm DEP_1.6.1.tar.gz DEP_1.6.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1545k  100 1545k    0     0  5475k      0 --:--:-- --:--:-- --:--:-- 5598k

install for i386

* 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
  converting help for package 'DEP'
    finding HTML links ... done
    DEP                                     html  
    DiUbi                                   html  
    DiUbi_ExpDesign                         html  
    LFQ                                     html  
    TMT                                     html  
    UbiLength                               html  
    UbiLength_ExpDesign                     html  
    add_rejections                          html  
    analyze_dep                             html  
    filter_missval                          html  
    filter_proteins                         html  
    get_df_long                             html  
    get_df_wide                             html  
    get_prefix                              html  
    get_results                             html  
    get_suffix                              html  
    import_IsobarQuant                      html  
    import_MaxQuant                         html  
    impute                                  html  
    make_se                                 html  
    make_se_parse                           html  
    make_unique                             html  
    manual_impute                           html  
    meanSdPlot                              html  
    normalize_vsn                           html  
    plot_all                                html  
    plot_cond                               html  
    plot_cond_freq                          html  
    plot_cond_overlap                       html  
    plot_cor                                html  
    plot_coverage                           html  
    plot_detect                             html  
    plot_dist                               html  
    plot_frequency                          html  
    plot_gsea                               html  
    plot_heatmap                            html  
    plot_imputation                         html  
    plot_missval                            html  
    plot_normalization                      html  
    plot_numbers                            html  
    plot_p_hist                             html  
    plot_pca                                html  
    plot_single                             html  
    plot_volcano                            html  
    process                                 html  
    report                                  html  
    run_app                                 html  
    se2msn                                  html  
    test_diff                               html  
    test_gsea                               html  
    theme_DEP1                              html  
    theme_DEP2                              html  
** 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

install for x64

* installing *source* package 'DEP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEP' as DEP_1.6.1.zip
* DONE (DEP)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DEP' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  34.78    1.40   39.00


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  53.01    0.73   56.28

name	user	system	elapsed
LFQ	1.82	0.09	1.94
TMT	0	0	0
add_rejections	0.81	0.09	0.90
analyze_dep	1.44	0.11	1.55
filter_missval	0.33	0.00	0.33
filter_proteins	0.19	0.00	0.19
get_df_long	1.20	0.02	1.21
get_df_wide	0.68	0.05	0.72
get_prefix	0	0	0
get_results	0.78	0.00	0.78
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.03	0.00	0.03
impute	1.08	0.00	1.08
make_se	0.06	0.00	0.06
make_se_parse	0.09	0.01	0.11
make_unique	0.03	0.00	0.03
manual_impute	0.74	0.00	0.74
meanSdPlot	0.53	0.02	0.55
normalize_vsn	0.30	0.00	0.29
plot_all	1.14	0.03	1.17
plot_cond	1.01	0.00	1.02
plot_cond_freq	0.75	0.00	0.75
plot_cond_overlap	1.00	0.01	1.02
plot_cor	1.47	0.00	1.86
plot_coverage	0.5	0.0	0.5
plot_detect	0.66	0.02	0.67
plot_dist	3.03	0.19	3.22
plot_frequency	0.28	0.03	0.31
plot_gsea	0.66	0.03	0.69
plot_heatmap	2.76	0.01	2.78
plot_imputation	1.05	0.06	1.11
plot_missval	1.31	0.05	1.36
plot_normalization	1.11	0.02	1.13
plot_numbers	0.36	0.01	0.38
plot_p_hist	1.32	0.00	1.33
plot_pca	1.24	0.00	1.23
plot_single	1.41	0.03	1.44
plot_volcano	5.79	0.03	5.83
process	1.06	0.00	1.06
report	0	0	0
run_app	0	0	0
se2msn	0.09	0.00	0.10
test_diff	0.85	0.02	0.86
test_gsea	0.65	0.02	0.67
theme_DEP1	0.28	0.00	0.29
theme_DEP2	0.38	0.00	0.37

name	user	system	elapsed
LFQ	1.61	0.09	1.70
TMT	0	0	0
add_rejections	0.81	0.02	0.82
analyze_dep	1.61	0.04	1.66
filter_missval	0.29	0.00	0.30
filter_proteins	0.19	0.00	0.18
get_df_long	0.66	0.03	0.69
get_df_wide	1.17	0.04	1.21
get_prefix	0	0	0
get_results	0.73	0.00	0.73
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.04	0.01	0.05
impute	1.04	0.02	1.06
make_se	0.03	0.00	0.03
make_se_parse	0.05	0.01	0.06
make_unique	0.02	0.00	0.02
manual_impute	0.51	0.00	0.51
meanSdPlot	0.49	0.02	0.50
normalize_vsn	0.26	0.00	0.27
plot_all	1.24	0.01	1.25
plot_cond	1.06	0.05	1.11
plot_cond_freq	0.83	0.00	0.83
plot_cond_overlap	0.79	0.05	0.84
plot_cor	1.11	0.01	1.13
plot_coverage	0.48	0.00	0.49
plot_detect	0.60	0.05	0.64
plot_dist	3.25	0.03	3.28
plot_frequency	0.29	0.00	0.29
plot_gsea	0.68	0.02	0.69
plot_heatmap	2.56	0.01	2.58
plot_imputation	1.35	0.02	1.36
plot_missval	1.33	0.00	1.32
plot_normalization	1.75	0.00	1.75
plot_numbers	0.43	0.00	0.44
plot_p_hist	1.55	0.00	1.55
plot_pca	1.32	0.03	1.36
plot_single	1.56	0.02	1.58
plot_volcano	5.09	0.03	5.13
process	1.20	0.01	1.22
report	0	0	0
run_app	0	0	0
se2msn	0.11	0.00	0.11
test_diff	1.20	0.02	1.22
test_gsea	0.75	0.03	0.78
theme_DEP1	0.33	0.00	0.33
theme_DEP2	0.47	0.00	0.47

CHECK report for DEP on tokay2

Summary

Command output

Installation output

Tests output

Example timings