Multiple platform build/check report for BioC 3.10

Package: DEP

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DEP_1.8.0.tar.gz

StartedAt: 2020-04-15 02:35:44 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:44:09 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 504.7 seconds

RetCode: 0

Status: OK

CheckDir: DEP.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings DEP_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/DEP.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.8.0'
* 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 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 5.92   0.02    5.93
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_volcano 5.71   0.01    5.72
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/DEP_1.8.0.tar.gz && rm -rf DEP.buildbin-libdir && mkdir DEP.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEP.buildbin-libdir DEP_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL DEP_1.8.0.zip && rm DEP_1.8.0.tar.gz DEP_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1542k  100 1542k    0     0  12.8M      0 --:--:-- --:--:-- --:--:-- 13.3M

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_1.8.0.zip
* DONE (DEP)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'DEP' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  40.32    1.70   44.64


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  62.59    0.82   65.65

name	user	system	elapsed
LFQ	1.11	0.11	1.22
TMT	0	0	0
add_rejections	1.37	0.06	1.44
analyze_dep	1.76	0.03	1.81
filter_missval	0.30	0.02	0.31
filter_proteins	0.2	0.0	0.2
get_df_long	0.77	0.00	0.77
get_df_wide	0.75	0.01	0.76
get_prefix	0	0	0
get_results	0.83	0.02	0.84
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.05	0.00	0.05
impute	1.09	0.01	1.11
make_se	0.03	0.00	0.03
make_se_parse	0.07	0.00	0.06
make_unique	0.01	0.00	0.02
manual_impute	0.53	0.01	0.54
meanSdPlot	0.57	0.00	0.56
normalize_vsn	0.34	0.00	0.35
plot_all	1.33	0.02	1.34
plot_cond	1.04	0.03	1.08
plot_cond_freq	0.87	0.02	0.89
plot_cond_overlap	0.88	0.00	0.87
plot_cor	1.61	0.09	1.70
plot_coverage	0.48	0.03	0.52
plot_detect	0.64	0.10	0.73
plot_dist	3.13	0.03	3.16
plot_frequency	0.31	0.00	0.31
plot_gsea	0.97	0.00	0.97
plot_heatmap	3.03	0.00	3.03
plot_imputation	1.72	0.04	1.77
plot_missval	1.09	0.05	1.14
plot_normalization	1.79	0.03	1.83
plot_numbers	0.4	0.0	0.4
plot_p_hist	1.42	0.02	1.44
plot_pca	1.27	0.00	1.27
plot_single	1.45	0.01	1.47
plot_volcano	5.92	0.02	5.93
process	1.32	0.01	1.33
report	0	0	0
run_app	0	0	0
se2msn	0.09	0.00	0.10
test_diff	1.30	0.02	1.31
test_gsea	0.81	0.02	0.83
theme_DEP1	0.41	0.00	0.40
theme_DEP2	0.67	0.00	0.67

name	user	system	elapsed
LFQ	1.78	0.04	1.83
TMT	0	0	0
add_rejections	0.85	0.04	0.89
analyze_dep	1.99	0.01	2.00
filter_missval	0.34	0.00	0.34
filter_proteins	0.22	0.00	0.22
get_df_long	1.41	0.05	1.45
get_df_wide	0.73	0.01	0.75
get_prefix	0.02	0.00	0.02
get_results	0.84	0.00	0.84
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.05	0.00	0.05
impute	1.67	0.03	1.70
make_se	0.06	0.00	0.06
make_se_parse	0.12	0.00	0.13
make_unique	0.03	0.00	0.03
manual_impute	0.97	0.00	0.97
meanSdPlot	0.96	0.02	0.97
normalize_vsn	0.45	0.03	0.48
plot_all	2.47	0.02	2.48
plot_cond	1.87	0.03	1.91
plot_cond_freq	1.49	0.01	1.50
plot_cond_overlap	1.46	0.04	1.48
plot_cor	1.94	0.03	1.97
plot_coverage	0.84	0.00	0.84
plot_detect	0.73	0.00	0.74
plot_dist	4.96	0.04	5.00
plot_frequency	0.55	0.00	0.55
plot_gsea	1.25	0.02	1.26
plot_heatmap	4.22	0.01	4.23
plot_imputation	3.15	0.04	3.17
plot_missval	2.03	0.01	2.05
plot_normalization	2.18	0.02	2.20
plot_numbers	0.77	0.00	0.77
plot_p_hist	2.69	0.03	2.71
plot_pca	2.38	0.00	2.38
plot_single	2.28	0.05	2.32
plot_volcano	5.71	0.01	5.72
process	2.15	0.00	2.15
report	0	0	0
run_app	0	0	0
se2msn	0.16	0.00	0.16
test_diff	1.53	0.02	1.55
test_gsea	1.26	0.01	1.28
theme_DEP1	0.58	0.02	0.60
theme_DEP2	0.75	0.01	0.76

CHECK report for DEP on tokay1

Summary

Command output

Installation output

Tests output

Example timings