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CHECK report for DEP on tokay1

This page was generated on 2018-04-12 13:30:16 -0400 (Thu, 12 Apr 2018).

Package 352/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEP 1.0.1
Arne Smits
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DEP
Branch: RELEASE_3_6
Last Commit: 471c4fa
Last Changed Date: 2017-11-17 03:14:10 -0400 (Fri, 17 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEP
Version: 1.0.1
Command: rm -rf DEP.buildbin-libdir DEP.Rcheck && mkdir DEP.buildbin-libdir DEP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEP.buildbin-libdir DEP_1.0.1.tar.gz >DEP.Rcheck\00install.out 2>&1 && cp DEP.Rcheck\00install.out DEP-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DEP.buildbin-libdir --install="check:DEP-install.out" --force-multiarch --no-vignettes --timings DEP_1.0.1.tar.gz
StartedAt: 2018-04-11 23:26:27 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:34:22 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 475.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DEP.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DEP.buildbin-libdir DEP.Rcheck && mkdir DEP.buildbin-libdir DEP.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DEP.buildbin-libdir DEP_1.0.1.tar.gz >DEP.Rcheck\00install.out 2>&1 && cp DEP.Rcheck\00install.out DEP-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DEP.buildbin-libdir --install="check:DEP-install.out" --force-multiarch --no-vignettes --timings DEP_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEP.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.0.1'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/LFQ.Rd:23: missing file link 'impute'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/TMT.Rd:22: missing file link 'impute'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/analyze_dep.Rd:52: missing file link 'limma'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/impute.Rd:20: missing file link 'impute'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/impute.Rd:23: missing file link 'impute'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/meanSdPlot.Rd:33: missing file link 'stat_binhex'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/meanSdPlot.Rd:37: missing file link 'stat_binhex'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/plot_cor.Rd:25: missing file link 'brewer.pal'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/process.Rd:25: missing file link 'impute'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/process.Rd:28: missing file link 'impute'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/report.Rd:14: missing file link 'rmarkdown'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/test_diff.Rd:43: missing file link 'limma'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DEP.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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_heatmap 6.17   0.02    6.18
plot_volcano 5.43   0.05    5.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_heatmap 11.43   0.07   11.48
plot_volcano  5.92   0.00    5.92
LFQ           5.53   0.17    5.81
analyze_dep   5.25   0.04    5.30
* 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-3.6-bioc/meat/DEP.Rcheck/00check.log'
for details.

Installation output

DEP.Rcheck/00install.out


install for i386

* installing *source* package 'DEP' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/LFQ.Rd:23: missing file link 'impute'
    TMT                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/TMT.Rd:22: missing file link 'impute'
    UbiLength                               html  
    UbiLength_ExpDesign                     html  
    add_rejections                          html  
    analyze_dep                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/analyze_dep.Rd:52: missing file link 'limma'
    filter_missval                          html  
    get_df_long                             html  
    get_df_wide                             html  
    get_prefix                              html  
    get_results                             html  
    import_IsobarQuant                      html  
    import_MaxQuant                         html  
    impute                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/impute.Rd:20: missing file link 'impute'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/impute.Rd:23: missing file link 'impute'
    make_se                                 html  
    make_se_parse                           html  
    make_unique                             html  
    manual_impute                           html  
    meanSdPlot                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/meanSdPlot.Rd:33: missing file link 'stat_binhex'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/meanSdPlot.Rd:37: missing file link 'stat_binhex'
    normalize_vsn                           html  
    plot_all                                html  
    plot_cond                               html  
    plot_cond_freq                          html  
    plot_cond_overlap                       html  
    plot_cor                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/plot_cor.Rd:25: missing file link 'brewer.pal'
    plot_coverage                           html  
    plot_detect                             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  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/process.Rd:25: missing file link 'impute'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/process.Rd:28: missing file link 'impute'
    report                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/report.Rd:14: missing file link 'rmarkdown'
    run_app                                 html  
    se2msn                                  html  
    test_diff                               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCOCKwa/R.INSTALLd7cce75c27/DEP/man/test_diff.Rd:43: missing file link 'limma'
    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_1.0.1.zip
* DONE (DEP)
In R CMD INSTALL
In R CMD INSTALL

Tests output

DEP.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
== testthat results  ===========================================================
OK: 290 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  40.64    0.51   43.20

DEP.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
[1] 0.2664646
== testthat results  ===========================================================
OK: 290 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  52.43    0.46   55.45

Example timings

DEP.Rcheck/examples_i386/DEP-Ex.timings

nameusersystemelapsed
LFQ4.350.204.90
TMT000
add_rejections1.860.051.90
analyze_dep3.160.063.24
filter_missval0.790.030.83
get_df_long0.940.061.00
get_df_wide0.980.021.00
get_prefix000
get_results1.150.011.17
import_IsobarQuant000
import_MaxQuant0.080.000.08
impute1.500.021.54
make_se0.050.000.05
make_se_parse0.090.000.09
make_unique0.020.000.02
manual_impute0.560.020.58
meanSdPlot1.520.011.53
normalize_vsn0.510.000.52
plot_all1.990.022.00
plot_cond1.620.001.62
plot_cond_freq1.160.001.16
plot_cond_overlap1.390.001.39
plot_cor1.930.011.94
plot_coverage0.940.000.93
plot_detect0.890.000.89
plot_frequency0.550.000.55
plot_gsea0.980.000.99
plot_heatmap6.170.026.18
plot_imputation1.390.001.39
plot_missval202
plot_normalization1.720.011.73
plot_numbers0.590.000.60
plot_p_hist1.700.031.73
plot_pca1.970.001.97
plot_single2.530.022.55
plot_volcano5.430.055.47
process1.840.001.84
report000
run_app000
se2msn0.080.000.08
test_diff1.510.031.54
test_gsea1.140.031.18
theme_DEP10.580.020.59
theme_DEP20.640.000.64

DEP.Rcheck/examples_x64/DEP-Ex.timings

nameusersystemelapsed
LFQ5.530.175.81
TMT000
add_rejections3.460.053.50
analyze_dep5.250.045.30
filter_missval2.450.002.45
get_df_long1.970.021.99
get_df_wide2.020.032.04
get_prefix0.010.000.02
get_results2.430.032.45
import_IsobarQuant000
import_MaxQuant0.750.000.75
impute2.330.002.37
make_se0.080.000.08
make_se_parse0.210.000.20
make_unique0.040.000.05
manual_impute1.220.021.23
meanSdPlot1.810.001.81
normalize_vsn0.710.000.71
plot_all3.560.003.56
plot_cond1.500.031.53
plot_cond_freq1.890.001.89
plot_cond_overlap1.560.011.58
plot_cor3.700.023.72
plot_coverage1.080.001.08
plot_detect1.670.001.67
plot_frequency1.240.001.24
plot_gsea2.560.012.57
plot_heatmap11.43 0.0711.48
plot_imputation3.250.083.33
plot_missval3.520.003.51
plot_normalization2.340.012.36
plot_numbers1.30.01.3
plot_p_hist3.840.023.86
plot_pca2.090.042.14
plot_single3.100.033.12
plot_volcano5.920.005.92
process2.070.002.06
report000
run_app000
se2msn0.090.000.09
test_diff2.310.022.33
test_gsea1.420.001.42
theme_DEP11.220.001.21
theme_DEP20.840.000.85