Multiple platform build/check report for BioC 3.12

Package: DEP

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEP_1.12.0.tar.gz

StartedAt: 2021-05-06 02:06:57 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 02:16:48 -0400 (Thu, 06 May 2021)

EllapsedTime: 591.3 seconds

RetCode: 0

Status: OK

CheckDir: DEP.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEP_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DEP.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.12.0'
* 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 (user + system) or elapsed time > 5s
          user system elapsed
plot_dist 6.34   0.03    6.39
LFQ       3.41   0.08    5.58
** running examples for arch 'x64' ... OK
* 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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/DEP_1.12.0.tar.gz && rm -rf DEP.buildbin-libdir && mkdir DEP.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEP.buildbin-libdir DEP_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DEP_1.12.0.zip && rm DEP_1.12.0.tar.gz DEP_1.12.0.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
100 1543k  100 1543k    0     0  24.0M      0 --:--:-- --:--:-- --:--:-- 24.3M

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_1.12.0.zip
* DONE (DEP)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DEP' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  51.93    1.57   58.56


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
pdfcrop.exe: MiKTeX encountered an internal error.
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  62.32    0.82   67.29

name	user	system	elapsed
LFQ	3.41	0.08	5.58
TMT	0	0	0
add_rejections	1.89	0.15	2.54
analyze_dep	3.28	0.05	3.33
filter_missval	0.62	0.02	0.64
filter_proteins	0.36	0.00	0.36
get_df_long	1.34	0.39	1.73
get_df_wide	1.60	0.04	1.64
get_prefix	0.01	0.00	0.02
get_results	1.96	0.04	1.98
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.09	0.00	0.10
impute	2.25	0.00	2.25
make_se	0.04	0.00	0.05
make_se_parse	0.07	0.00	0.06
make_unique	0.01	0.00	0.02
manual_impute	1.26	0.00	1.27
meanSdPlot	1.3	0.0	1.3
normalize_vsn	0.75	0.00	0.75
plot_all	1.62	0.00	1.62
plot_cond	2.00	0.07	2.08
plot_cond_freq	1.99	0.02	2.00
plot_cond_overlap	1.69	0.01	1.70
plot_cor	2.67	0.07	2.74
plot_coverage	0.97	0.00	0.97
plot_detect	1.08	0.00	1.07
plot_dist	6.34	0.03	6.39
plot_frequency	0.84	0.00	0.85
plot_gsea	1.60	0.03	1.62
plot_heatmap	4.79	0.05	4.91
plot_imputation	2.41	0.03	2.44
plot_missval	2.64	0.01	2.65
plot_normalization	2.34	0.03	2.38
plot_numbers	0.96	0.00	0.95
plot_p_hist	2.73	0.02	2.75
plot_pca	2.50	0.02	2.52
plot_single	1.86	0.03	1.89
plot_volcano	4.69	0.01	4.70
process	2.40	0.00	2.41
report	0	0	0
run_app	0	0	0
se2msn	0.21	0.02	0.22
test_diff	1.75	0.01	1.76
test_gsea	1.07	0.02	1.07
theme_DEP1	0.64	0.00	0.65
theme_DEP2	0.79	0.00	0.79

name	user	system	elapsed
LFQ	1.94	0.02	1.95
TMT	0	0	0
add_rejections	2.14	0.00	2.14
analyze_dep	1.81	0.11	1.93
filter_missval	0.63	0.00	0.62
filter_proteins	0.36	0.00	0.36
get_df_long	0.95	0.03	0.99
get_df_wide	0.94	0.02	0.95
get_prefix	0	0	0
get_results	1.72	0.01	1.73
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.10	0.00	0.09
impute	1.87	0.08	1.96
make_se	0.05	0.00	0.04
make_se_parse	0.06	0.00	0.06
make_unique	0.02	0.00	0.02
manual_impute	0.76	0.00	0.77
meanSdPlot	0.69	0.00	0.68
normalize_vsn	0.43	0.00	0.42
plot_all	1.54	0.00	1.55
plot_cond	1.24	0.02	1.25
plot_cond_freq	1.09	0.00	1.09
plot_cond_overlap	1.02	0.01	1.03
plot_cor	1.58	0.02	1.60
plot_coverage	0.59	0.00	0.59
plot_detect	0.74	0.00	0.73
plot_dist	3.75	0.03	3.78
plot_frequency	0.44	0.00	0.44
plot_gsea	0.89	0.00	0.89
plot_heatmap	2.85	0.00	2.84
plot_imputation	1.24	0.00	1.24
plot_missval	1.75	0.00	1.75
plot_normalization	1.34	0.01	1.36
plot_numbers	0.55	0.00	0.55
plot_p_hist	1.56	0.02	1.57
plot_pca	1.41	0.00	1.41
plot_single	1.70	0.02	1.71
plot_volcano	4.30	0.03	4.33
process	1.45	0.00	1.46
report	0	0	0
run_app	0	0	0
se2msn	0.11	0.00	0.10
test_diff	1.25	0.01	1.27
test_gsea	1.36	0.02	1.37
theme_DEP1	0.81	0.01	0.83
theme_DEP2	0.95	0.00	0.95

CHECK report for DEP on tokay1

Summary

Command output

Installation output

Tests output

Example timings