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CHECK report for DEP on tokay1

This page was generated on 2019-04-13 11:28:09 -0400 (Sat, 13 Apr 2019).

Package 392/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.4.1
Arne Smits
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DEP
Branch: RELEASE_3_8
Last Commit: e024011
Last Changed Date: 2019-01-04 13:28:37 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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


Installation output

DEP.Rcheck/00install.out

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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
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
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

Tests output

DEP.Rcheck/tests_i386/testthat.Rout


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 

DEP.Rcheck/tests_x64/testthat.Rout


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 

Example timings

DEP.Rcheck/examples_i386/DEP-Ex.timings

nameusersystemelapsed
LFQ2.350.142.55
TMT000
add_rejections1.730.031.77
analyze_dep3.360.053.41
filter_missval1.530.001.53
filter_proteins0.50.00.5
get_df_long1.480.031.52
get_df_wide1.590.001.60
get_prefix0.000.000.01
get_results1.460.031.49
get_suffix000
import_IsobarQuant000
import_MaxQuant0.040.000.04
impute1.350.001.35
make_se0.040.000.04
make_se_parse0.070.000.07
make_unique0.010.000.01
manual_impute0.740.000.74
meanSdPlot1.090.001.09
normalize_vsn0.650.000.65
plot_all2.420.012.44
plot_cond1.610.031.64
plot_cond_freq1.610.021.63
plot_cond_overlap1.090.021.11
plot_cor1.830.001.83
plot_coverage0.630.030.65
plot_detect0.710.030.75
plot_dist2.440.052.49
plot_frequency0.380.060.44
plot_gsea0.860.000.86
plot_heatmap3.750.013.76
plot_imputation1.360.051.41
plot_missval1.870.001.87
plot_normalization1.450.001.46
plot_numbers0.490.000.48
plot_p_hist1.50.01.5
plot_pca1.620.001.63
plot_single1.990.001.98
plot_volcano7.020.027.03
process1.360.001.36
report000
run_app000
se2msn0.110.000.11
test_diff1.110.001.11
test_gsea0.970.031.00
theme_DEP10.370.000.37
theme_DEP20.470.000.47

DEP.Rcheck/examples_x64/DEP-Ex.timings

nameusersystemelapsed
LFQ1.280.011.29
TMT000
add_rejections1.470.031.50
analyze_dep1.870.101.97
filter_missval0.50.00.5
filter_proteins0.800.010.81
get_df_long0.840.000.84
get_df_wide0.840.020.86
get_prefix000
get_results0.970.011.00
get_suffix000
import_IsobarQuant000
import_MaxQuant0.050.000.05
impute1.280.031.31
make_se0.030.000.03
make_se_parse0.060.000.06
make_unique0.020.000.02
manual_impute0.620.000.62
meanSdPlot0.630.000.63
normalize_vsn0.370.000.37
plot_all1.610.021.63
plot_cond1.190.061.25
plot_cond_freq1.040.001.05
plot_cond_overlap1.220.011.23
plot_cor1.390.001.39
plot_coverage0.590.020.61
plot_detect0.740.010.75
plot_dist2.540.002.54
plot_frequency0.420.000.42
plot_gsea0.910.020.92
plot_heatmap4.230.004.24
plot_imputation2.030.002.03
plot_missval1.440.001.43
plot_normalization1.560.031.60
plot_numbers0.580.000.58
plot_p_hist2.390.002.39
plot_pca2.020.012.03
plot_single2.120.082.21
plot_volcano8.310.038.34
process2.390.002.39
report000
run_app000
se2msn0.090.000.09
test_diff1.110.021.13
test_gsea0.890.030.92
theme_DEP10.420.000.43
theme_DEP20.520.000.51