Multiple platform build/check report for BioC 3.14 - CHECK results for DEP on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: DEP

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DEP_1.16.0.tar.gz

StartedAt: 2022-04-12 18:27:22 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 18:36:09 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 526.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: DEP.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DEP_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DEP.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.16.0'
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
plot_volcano 5.72   0.05    5.77
plot_dist    5.25   0.08    5.70
** 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-3.14-bioc/meat/DEP.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DEP_1.16.0.tar.gz && rm -rf DEP.buildbin-libdir && mkdir DEP.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEP.buildbin-libdir DEP_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DEP_1.16.0.zip && rm DEP_1.16.0.tar.gz DEP_1.16.0.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
 20 1545k   20  318k    0     0   655k      0  0:00:02 --:--:--  0:00:02  654k
100 1545k  100 1545k    0     0  1123k      0  0:00:01  0:00:01 --:--:-- 1124k

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_1.16.0.zip
* DONE (DEP)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DEP' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  46.62    1.62   66.73


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  49.68    0.87   69.06

name	user	system	elapsed
LFQ	1.91	0.23	2.14
TMT	0	0	0
add_rejections	0.91	0.16	1.06
analyze_dep	2.57	0.02	2.60
filter_missval	0.82	0.00	0.81
filter_proteins	0.39	0.00	0.39
get_df_long	1.56	0.00	1.56
get_df_wide	0.91	0.07	0.99
get_prefix	0	0	0
get_results	1.04	0.02	1.06
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.06	0.00	0.06
impute	1.46	0.00	1.46
make_se	0.04	0.00	0.04
make_se_parse	0.08	0.00	0.08
make_unique	0.01	0.00	0.01
manual_impute	0.91	0.11	1.02
meanSdPlot	0.75	0.00	0.75
normalize_vsn	0.55	0.00	0.55
plot_all	1.62	0.08	1.70
plot_cond	1.19	0.01	1.20
plot_cond_freq	1.01	0.00	1.01
plot_cond_overlap	0.99	0.00	0.99
plot_cor	1.43	0.02	1.45
plot_coverage	0.97	0.00	1.23
plot_detect	1.31	0.00	1.55
plot_dist	5.25	0.08	5.70
plot_frequency	0.54	0.00	0.54
plot_gsea	0.87	0.03	0.90
plot_heatmap	3.39	0.00	3.41
plot_imputation	1.38	0.08	1.45
plot_missval	1.71	0.10	1.83
plot_normalization	1.36	0.02	1.37
plot_numbers	0.57	0.02	0.58
plot_p_hist	1.51	0.01	1.53
plot_pca	1.83	0.00	1.83
plot_single	2.31	0.00	2.31
plot_volcano	5.72	0.05	5.77
process	1.99	0.01	2.03
report	0	0	0
run_app	0	0	0
se2msn	0.14	0.00	0.14
test_diff	1.25	0.00	1.25
test_gsea	0.89	0.00	0.89
theme_DEP1	0.49	0.00	0.48
theme_DEP2	0.54	0.00	0.55

name	user	system	elapsed
LFQ	1.53	0.05	1.58
TMT	0	0	0
add_rejections	1.61	0.02	1.62
analyze_dep	2.42	0.07	2.50
filter_missval	0.67	0.00	0.67
filter_proteins	0.44	0.00	0.44
get_df_long	0.94	0.00	0.93
get_df_wide	0.89	0.00	0.89
get_prefix	0	0	0
get_results	1.08	0.00	1.08
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.06	0.00	0.07
impute	1.61	0.00	1.60
make_se	0.05	0.00	0.05
make_se_parse	0.08	0.00	0.08
make_unique	0.03	0.00	0.03
manual_impute	0.97	0.00	0.97
meanSdPlot	0.79	0.02	0.81
normalize_vsn	1.16	0.00	1.16
plot_all	2.11	0.02	2.13
plot_cond	1.27	0.00	1.26
plot_cond_freq	0.98	0.00	0.99
plot_cond_overlap	0.99	0.00	0.98
plot_cor	1.61	0.03	1.64
plot_coverage	0.69	0.00	0.69
plot_detect	0.89	0.00	0.89
plot_dist	4	0	4
plot_frequency	0.5	0.0	0.5
plot_gsea	0.87	0.00	0.88
plot_heatmap	2.92	0.00	2.92
plot_imputation	1.21	0.03	1.23
plot_missval	1.89	0.00	1.89
plot_normalization	1.45	0.00	1.46
plot_numbers	0.61	0.00	0.61
plot_p_hist	1.55	0.00	1.54
plot_pca	1.45	0.00	1.46
plot_single	1.64	0.00	1.64
plot_volcano	4.14	0.00	4.14
process	1.66	0.00	1.65
report	0	0	0
run_app	0	0	0
se2msn	0.14	0.00	0.14
test_diff	1.17	0.00	1.18
test_gsea	0.87	0.00	0.87
theme_DEP1	0.52	0.00	0.52
theme_DEP2	0.58	0.00	0.58

CHECK results for DEP on tokay2

Summary

Command output

Installation output

Tests output

Example timings