Multiple platform build/check report for BioC 3.13 - CHECK results for DEP on tokay2

Package: DEP

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DEP_1.14.0.tar.gz

StartedAt: 2021-10-14 22:07:49 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 22:16:24 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 515.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: DEP.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DEP_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DEP.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.14.0'
* 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 ... WARNING
Missing link or links in documentation object 'LFQ.Rd':
  '[MSnbase:impute-methods]{impute}'

Missing link or links in documentation object 'TMT.Rd':
  '[MSnbase:impute-methods]{impute}'

Missing link or links in documentation object 'impute.Rd':
  '[MSnbase:impute-methods]{impute}'

Missing link or links in documentation object 'process.Rd':
  '[MSnbase:impute-methods]{impute}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 LazyData ... 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
** 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/DEP.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DEP_1.14.0.tar.gz && rm -rf DEP.buildbin-libdir && mkdir DEP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEP.buildbin-libdir DEP_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DEP_1.14.0.zip && rm DEP_1.14.0.tar.gz DEP_1.14.0.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
  0 1543k    0 14875    0     0   124k      0  0:00:12 --:--:--  0:00:12  125k
100 1543k  100 1543k    0     0  2662k      0 --:--:-- --:--:-- --:--:-- 2661k

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_1.14.0.zip
* DONE (DEP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DEP' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  44.04    1.45   64.39


R version 4.1.1 (2021-08-10) -- "Kick Things"
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")
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  46.09    0.84   65.85

name	user	system	elapsed
LFQ	2.07	0.13	2.19
TMT	0	0	0
add_rejections	0.92	0.05	0.97
analyze_dep	2.58	0.10	2.69
filter_missval	0.63	0.13	0.75
filter_proteins	0.33	0.00	0.33
get_df_long	0.84	0.02	0.85
get_df_wide	0.82	0.01	0.84
get_prefix	0	0	0
get_results	1.05	0.02	1.07
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.06	0.00	0.06
impute	1.35	0.00	1.34
make_se	0.04	0.00	0.05
make_se_parse	0.10	0.00	0.09
make_unique	0.03	0.00	0.03
manual_impute	0.84	0.00	0.85
meanSdPlot	0.77	0.00	0.76
normalize_vsn	0.51	0.00	0.52
plot_all	1.91	0.01	1.92
plot_cond	1.19	0.02	1.20
plot_cond_freq	0.95	0.00	0.96
plot_cond_overlap	0.94	0.00	0.94
plot_cor	2.54	0.04	2.62
plot_coverage	1.07	0.00	1.06
plot_detect	1.48	0.15	1.63
plot_dist	4.99	0.00	5.00
plot_frequency	0.42	0.03	0.45
plot_gsea	0.83	0.00	0.83
plot_heatmap	2.54	0.03	2.58
plot_imputation	1.24	0.00	1.23
plot_missval	2.22	0.00	2.22
plot_normalization	1.32	0.03	1.36
plot_numbers	0.54	0.01	0.56
plot_p_hist	1.39	0.00	1.42
plot_pca	1.21	0.02	1.23
plot_single	2.50	0.01	4.86
plot_volcano	4.40	0.03	4.78
process	1.46	0.02	1.49
report	0	0	0
run_app	0	0	0
se2msn	0.11	0.00	0.11
test_diff	1.06	0.00	1.07
test_gsea	0.80	0.00	0.79
theme_DEP1	0.44	0.00	0.44
theme_DEP2	0.53	0.00	0.53

name	user	system	elapsed
LFQ	1.21	0.04	1.25
TMT	0	0	0
add_rejections	1.69	0.00	1.69
analyze_dep	2.41	0.05	2.46
filter_missval	0.6	0.0	0.6
filter_proteins	0.41	0.00	0.41
get_df_long	0.86	0.02	0.88
get_df_wide	0.86	0.00	0.86
get_prefix	0	0	0
get_results	0.97	0.00	0.97
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.05	0.00	0.05
impute	1.45	0.00	1.45
make_se	0.05	0.00	0.05
make_se_parse	0.07	0.00	0.07
make_unique	0.02	0.00	0.02
manual_impute	0.89	0.00	0.89
meanSdPlot	1.39	0.00	1.39
normalize_vsn	0.48	0.00	0.49
plot_all	1.67	0.06	1.74
plot_cond	1.19	0.00	1.19
plot_cond_freq	0.94	0.00	0.94
plot_cond_overlap	0.89	0.00	0.89
plot_cor	1.42	0.00	1.42
plot_coverage	0.62	0.00	0.62
plot_detect	0.77	0.00	0.77
plot_dist	3.81	0.00	3.81
plot_frequency	0.46	0.00	0.46
plot_gsea	0.84	0.00	0.84
plot_heatmap	2.8	0.0	2.8
plot_imputation	1.2	0.0	1.2
plot_missval	1.77	0.00	1.76
plot_normalization	1.40	0.00	1.41
plot_numbers	0.58	0.00	0.58
plot_p_hist	1.47	0.00	1.47
plot_pca	1.28	0.00	1.28
plot_single	1.45	0.00	1.45
plot_volcano	3.89	0.00	3.89
process	1.6	0.0	1.6
report	0	0	0
run_app	0	0	0
se2msn	0.12	0.02	0.14
test_diff	1.06	0.00	1.06
test_gsea	0.82	0.00	0.81
theme_DEP1	0.48	0.00	0.49
theme_DEP2	0.58	0.00	0.57

CHECK results for DEP on tokay2

Summary

Command output

Installation output

Tests output

Example timings