Multiple platform build/check report for BioC 3.8 - CHECK report for DEP on tokay1

Package: DEP

Version: 1.4.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEP_1.4.1.tar.gz

StartedAt: 2019-04-13 01:43:23 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:51:54 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 510.8 seconds

RetCode: 0

Status: OK

CheckDir: DEP.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEP_1.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DEP.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.4.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 7.02   0.02    7.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_volcano 8.31   0.03    8.34
* 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://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DEP_1.4.1.tar.gz && rm -rf DEP.buildbin-libdir && mkdir DEP.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEP.buildbin-libdir DEP_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DEP_1.4.1.zip && rm DEP_1.4.1.tar.gz DEP_1.4.1.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 1542k  100 1542k    0     0  24.1M      0 --:--:-- --:--:-- --:--:-- 25.9M

install for i386

* installing *source* package 'DEP' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'DEP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEP' as DEP_1.4.1.zip
* DONE (DEP)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DEP' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.3 (2019-03-11) -- "Great Truth"
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: 327 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  42.39    1.28   45.71


R version 3.5.3 (2019-03-11) -- "Great Truth"
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: 327 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  49.45    0.59   52.25

name	user	system	elapsed
LFQ	2.35	0.14	2.55
TMT	0	0	0
add_rejections	1.73	0.03	1.77
analyze_dep	3.36	0.05	3.41
filter_missval	1.53	0.00	1.53
filter_proteins	0.5	0.0	0.5
get_df_long	1.48	0.03	1.52
get_df_wide	1.59	0.00	1.60
get_prefix	0.00	0.00	0.01
get_results	1.46	0.03	1.49
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.04	0.00	0.04
impute	1.35	0.00	1.35
make_se	0.04	0.00	0.04
make_se_parse	0.07	0.00	0.07
make_unique	0.01	0.00	0.01
manual_impute	0.74	0.00	0.74
meanSdPlot	1.09	0.00	1.09
normalize_vsn	0.65	0.00	0.65
plot_all	2.42	0.01	2.44
plot_cond	1.61	0.03	1.64
plot_cond_freq	1.61	0.02	1.63
plot_cond_overlap	1.09	0.02	1.11
plot_cor	1.83	0.00	1.83
plot_coverage	0.63	0.03	0.65
plot_detect	0.71	0.03	0.75
plot_dist	2.44	0.05	2.49
plot_frequency	0.38	0.06	0.44
plot_gsea	0.86	0.00	0.86
plot_heatmap	3.75	0.01	3.76
plot_imputation	1.36	0.05	1.41
plot_missval	1.87	0.00	1.87
plot_normalization	1.45	0.00	1.46
plot_numbers	0.49	0.00	0.48
plot_p_hist	1.5	0.0	1.5
plot_pca	1.62	0.00	1.63
plot_single	1.99	0.00	1.98
plot_volcano	7.02	0.02	7.03
process	1.36	0.00	1.36
report	0	0	0
run_app	0	0	0
se2msn	0.11	0.00	0.11
test_diff	1.11	0.00	1.11
test_gsea	0.97	0.03	1.00
theme_DEP1	0.37	0.00	0.37
theme_DEP2	0.47	0.00	0.47

name	user	system	elapsed
LFQ	1.28	0.01	1.29
TMT	0	0	0
add_rejections	1.47	0.03	1.50
analyze_dep	1.87	0.10	1.97
filter_missval	0.5	0.0	0.5
filter_proteins	0.80	0.01	0.81
get_df_long	0.84	0.00	0.84
get_df_wide	0.84	0.02	0.86
get_prefix	0	0	0
get_results	0.97	0.01	1.00
get_suffix	0	0	0
import_IsobarQuant	0	0	0
import_MaxQuant	0.05	0.00	0.05
impute	1.28	0.03	1.31
make_se	0.03	0.00	0.03
make_se_parse	0.06	0.00	0.06
make_unique	0.02	0.00	0.02
manual_impute	0.62	0.00	0.62
meanSdPlot	0.63	0.00	0.63
normalize_vsn	0.37	0.00	0.37
plot_all	1.61	0.02	1.63
plot_cond	1.19	0.06	1.25
plot_cond_freq	1.04	0.00	1.05
plot_cond_overlap	1.22	0.01	1.23
plot_cor	1.39	0.00	1.39
plot_coverage	0.59	0.02	0.61
plot_detect	0.74	0.01	0.75
plot_dist	2.54	0.00	2.54
plot_frequency	0.42	0.00	0.42
plot_gsea	0.91	0.02	0.92
plot_heatmap	4.23	0.00	4.24
plot_imputation	2.03	0.00	2.03
plot_missval	1.44	0.00	1.43
plot_normalization	1.56	0.03	1.60
plot_numbers	0.58	0.00	0.58
plot_p_hist	2.39	0.00	2.39
plot_pca	2.02	0.01	2.03
plot_single	2.12	0.08	2.21
plot_volcano	8.31	0.03	8.34
process	2.39	0.00	2.39
report	0	0	0
run_app	0	0	0
se2msn	0.09	0.00	0.09
test_diff	1.11	0.02	1.13
test_gsea	0.89	0.03	0.92
theme_DEP1	0.42	0.00	0.43
theme_DEP2	0.52	0.00	0.51

CHECK report for DEP on tokay1

Summary

Command output

Installation output

Tests output

Example timings