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CHECK report for iCOBRA on tokay2

This page was generated on 2020-10-17 11:56:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE iCOBRA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 853/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCOBRA 1.16.0
Charlotte Soneson
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/iCOBRA
Branch: RELEASE_3_11
Last Commit: 43f9f59
Last Changed Date: 2020-04-27 14:52:54 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: iCOBRA
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCOBRA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings iCOBRA_1.16.0.tar.gz
StartedAt: 2020-10-17 05:08:26 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:12:31 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 244.9 seconds
RetCode: 0
Status:  OK  
CheckDir: iCOBRA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:iCOBRA.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings iCOBRA_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/iCOBRA.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iCOBRA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iCOBRA' version '1.16.0'
* 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 'iCOBRA' 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 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: OK

Installation output

iCOBRA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/iCOBRA_1.16.0.tar.gz && rm -rf iCOBRA.buildbin-libdir && mkdir iCOBRA.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=iCOBRA.buildbin-libdir iCOBRA_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL iCOBRA_1.16.0.zip && rm iCOBRA_1.16.0.tar.gz iCOBRA_1.16.0.zip
###
##############################################################################
##############################################################################


  % 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 2499k  100 2499k    0     0  23.1M      0 --:--:-- --:--:-- --:--:-- 24.6M

install for i386

* installing *source* package 'iCOBRA' ...
** 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 'iCOBRA'
    finding HTML links ... done
    COBRAData                               html  
    COBRAPerformance                        html  
    COBRAPlot                               html  
    COBRAapp                                html  
    Extract                                 html  
    basemethods                             html  
    calculate_adjp                          html  
    calculate_performance                   html  
    cobradata_example                       html  
    cobradata_example_sval                  html  
    coerce                                  html  
    corr                                    html  
    deviation                               html  
    facetted                                html  
    fdrnbr                                  html  
    fdrnbrcurve                             html  
    fdrtpr                                  html  
    fdrtprcurve                             html  
    fpc                                     html  
    fpr                                     html  
    fsrnbr                                  html  
    fsrnbrcurve                             html  
    maxsplit                                html  
    onlyshared                              html  
    overlap                                 html  
    padj                                    html  
    plot_corr                               html  
    plot_deviation                          html  
    plot_fdrnbrcurve                        html  
    plot_fdrtprcurve                        html  
    plot_fpc                                html  
    plot_fpr                                html  
    plot_fsrnbrcurve                        html  
    plot_overlap                            html  
    plot_roc                                html  
    plot_scatter                            html  
    plot_tpr                                html  
    plot_upset                              html  
    plotcolors                              html  
    prepare_data_for_plot                   html  
    pval                                    html  
    reorder_levels                          html  
    roc                                     html  
    scatter                                 html  
    score                                   html  
    splv                                    html  
    stratiflevels                           html  
    sval                                    html  
    tpr                                     html  
    truth                                   html  
    update_cobradata                        html  
    update_cobraperformance                 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 'iCOBRA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iCOBRA' as iCOBRA_1.16.0.zip
* DONE (iCOBRA)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'iCOBRA' successfully unpacked and MD5 sums checked

Tests output

iCOBRA.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(iCOBRA)
> 
> test_check("iCOBRA")
An object of class "COBRAData"
@pval
                   Method1     Method2     Method3
ENSG00000000457 0.01446441 0.008665558 0.003317162
ENSG00000000460 0.95247473 0.927616428 0.974301159
ENSG00000000938 0.74556923 0.632987431 0.639716304
ENSG00000000971 0.72582371 0.568683774 0.610769221
ENSG00000001460 0.64292689 0.629807292 0.613039563
2413 more rows ...

@padj
                   Method1    Method2
ENSG00000000457 0.05544853 0.03916508
ENSG00000000460 0.98752284 0.96680023
ENSG00000000938 0.91465571 0.82867282
ENSG00000000971 0.90618247 0.79410144
ENSG00000001460 0.87662457 0.82779499
2413 more rows ...

@sval
                   Method1    Method2
ENSG00000000457 0.05544853 0.03916508
ENSG00000000460 0.98752284 0.96680023
ENSG00000000938 0.91465571 0.82867282
ENSG00000000971 0.90618247 0.79410144
ENSG00000001460 0.87662457 0.82779499
2413 more rows ...

@score
                    Method1     Method2      Method3
ENSG00000000457 -0.76274305 -0.75783824 -0.743951068
ENSG00000000460 -0.02033394 -0.02096682 -0.007355491
ENSG00000000938  0.10235482  0.10968180  0.113127202
ENSG00000000971 -0.12495998 -0.12090589 -0.112072431
ENSG00000001460 -0.16319682 -0.13257307 -0.149343205
2413 more rows ...

@truth
                status n_isoforms      logFC     logFC_cat       expr
ENSG00000000457      0          5  0.0000000 [ 0.00, 0.56)   8.525774
ENSG00000000460      1         10  1.1643146 [ 0.56, 1.54)   5.371661
ENSG00000000938      0          8  0.0000000 [ 0.00, 0.56)  11.543626
ENSG00000000971      0          6  0.0000000 [ 0.00, 0.56) 163.547797
ENSG00000001460      1         13 -0.1033807 [ 0.00, 0.56)   6.874695
                           expr_cat
ENSG00000000457 [   2.628,  17.148)
ENSG00000000460 [   2.628,  17.148)
ENSG00000000938 [   2.628,  17.148)
ENSG00000000971 [  17.148,3265.406]
ENSG00000001460 [   2.628,  17.148)
3853 more rows ...

An object of class "COBRAPerformance"
@fdrtpr
data frame with 0 columns and 0 rows

@fdrtprcurve
data frame with 0 columns and 0 rows

@fdrnbr
data frame with 0 columns and 0 rows

@fdrnbrcurve
data frame with 0 columns and 0 rows

@fsrnbr
data frame with 0 columns and 0 rows

@fsrnbrcurve
data frame with 0 columns and 0 rows

@deviation
data frame with 0 columns and 0 rows

@tpr
      thr  method basemethod   meas      fullmethod splitval NBR  TP  FP   TN
1 thr0.01 Method1    Method1 __padj Method1_overall  overall 508 387 121 1473
2 thr0.01 Method2    Method2 __padj Method2_overall  overall 392 308  84 1510
3 thr0.05 Method1    Method1 __padj Method1_overall  overall 620 448 172 1422
4 thr0.05 Method2    Method2 __padj Method2_overall  overall 565 406 159 1435
5  thr0.1 Method1    Method1 __padj Method1_overall  overall 697 478 219 1375
6  thr0.1 Method2    Method2 __padj Method2_overall  overall 651 448 203 1391
   FN TOT_CALLED DIFF NONDIFF       TPR
1 437       2418  842    3016 0.4596200
2 516       2418  842    3016 0.3657957
3 376       2418  842    3016 0.5320665
4 418       2418  842    3016 0.4821853
5 346       2418  842    3016 0.5676960
6 376       2418  842    3016 0.5320665

@fpr
data frame with 0 columns and 0 rows

@roc
data frame with 0 columns and 0 rows

@scatter
data frame with 0 columns and 0 rows

@fpc
data frame with 0 columns and 0 rows

@overlap
data frame with 0 columns and 0 rows

@corr
data frame with 0 columns and 0 rows

@maxsplit
[1] 3

@splv
[1] "none"

@onlyshared
[1] FALSE

An object of class "COBRAPerformance"
@fdrtpr
data frame with 0 columns and 0 rows

@fdrtprcurve
data frame with 0 columns and 0 rows

@fdrnbr
data frame with 0 columns and 0 rows

@fdrnbrcurve
data frame with 0 columns and 0 rows

@fsrnbr
data frame with 0 columns and 0 rows

@fsrnbrcurve
data frame with 0 columns and 0 rows

@deviation
data frame with 0 columns and 0 rows

@tpr
      thr  method basemethod   meas                           fullmethod
1 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.000,   0.362)
2 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.362,   2.628)
3 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   2.628,  17.148)
4 thr0.01 Method1    Method1 __padj Method1_expr_cat:[  17.148,3265.406]
5 thr0.01 Method1    Method1 __padj                      Method1_overall
                      splitval NBR  TP  FP   TN  FN TOT_CALLED DIFF NONDIFF
1 expr_cat:[   0.000,   0.362)  18  12   6  341  12        371   30    1747
2 expr_cat:[   0.362,   2.628) 112 100  12  374 175        661  287     406
3 expr_cat:[   2.628,  17.148) 157 102  55  414 121        692  223     471
4 expr_cat:[  17.148,3265.406] 221 173  48  344 129        694  302     392
5                      overall 508 387 121 1473 437       2418  842    3016
        TPR
1 0.4000000
2 0.3484321
3 0.4573991
4 0.5728477
5 0.4596200
25 more rows ...

@fpr
data frame with 0 columns and 0 rows

@roc
data frame with 0 columns and 0 rows

@scatter
data frame with 0 columns and 0 rows

@fpc
data frame with 0 columns and 0 rows

@overlap
$[   0.000,   0.362)
                Method1 Method2 truth
ENSG00000007908       0       0     0
ENSG00000008118       0       0     0
ENSG00000042781       0       0     0
ENSG00000049247       0       0     1
ENSG00000057468       0       0     0
1772 more rows ...

$[   2.628,  17.148)
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000001460       0       0     1
ENSG00000006555       0       0     1
689 more rows ...

$[  17.148,3265.406]
                Method1 Method2 truth
ENSG00000000971       0       0     0
ENSG00000001461       0       0     0
ENSG00000004455       1       1     0
ENSG00000004487       0       0     1
ENSG00000007923       0       0     0
689 more rows ...

$[   0.362,   2.628)
                Method1 Method2 truth
ENSG00000007933       0       0     0
ENSG00000007968       1       1     0
ENSG00000009724       0       0     0
ENSG00000010932       0       0     1
ENSG00000024526       1       1     1
688 more rows ...

$overall
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000000971       0       0     0
ENSG00000001460       0       0     1
3853 more rows ...


@corr
data frame with 0 columns and 0 rows

@maxsplit
[1] 4

@splv
[1] "expr_cat"

@onlyshared
[1] FALSE

An object of class "COBRAPlot"
@plotcolors
                             Method1                              Method2 
                           "#00ACFC"                            "#8B93FF" 
                               truth Method1_expr_cat:[   0.000,   0.362) 
                           "#FF65AC"                            "#F8766D" 
Method2_expr_cat:[   0.000,   0.362) 
                           "#E18A00" 
58 more elements ...

@facetted
[1] FALSE

@fdrtpr
data frame with 0 columns and 0 rows

@fdrtprcurve
data frame with 0 columns and 0 rows

@fdrnbr
data frame with 0 columns and 0 rows

@fdrnbrcurve
data frame with 0 columns and 0 rows

@fsrnbr
data frame with 0 columns and 0 rows

@fsrnbrcurve
data frame with 0 columns and 0 rows

@deviation
data frame with 0 columns and 0 rows

@tpr
      thr  method basemethod   meas                           fullmethod
1 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.000,   0.362)
2 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.362,   2.628)
3 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   2.628,  17.148)
4 thr0.01 Method1    Method1 __padj Method1_expr_cat:[  17.148,3265.406]
5 thr0.01 Method1    Method1 __padj                      Method1_overall
                      splitval NBR  TP  FP   TN  FN TOT_CALLED DIFF NONDIFF
1 expr_cat:[   0.000,   0.362)  18  12   6  341  12        371   30    1747
2 expr_cat:[   0.362,   2.628) 112 100  12  374 175        661  287     406
3 expr_cat:[   2.628,  17.148) 157 102  55  414 121        692  223     471
4 expr_cat:[  17.148,3265.406] 221 173  48  344 129        694  302     392
5                      overall 508 387 121 1473 437       2418  842    3016
        TPR num_method
1 0.4000000          1
2 0.3484321          2
3 0.4573991          3
4 0.5728477          4
5 0.4596200          5
25 more rows ...

@fpr
data frame with 0 columns and 0 rows

@roc
data frame with 0 columns and 0 rows

@scatter
data frame with 0 columns and 0 rows

@fpc
data frame with 0 columns and 0 rows

@overlap
$[   0.000,   0.362)
                Method1 Method2 truth
ENSG00000007908       0       0     0
ENSG00000008118       0       0     0
ENSG00000042781       0       0     0
ENSG00000049247       0       0     1
ENSG00000057468       0       0     0
1772 more rows ...

$[   2.628,  17.148)
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000001460       0       0     1
ENSG00000006555       0       0     1
689 more rows ...

$[  17.148,3265.406]
                Method1 Method2 truth
ENSG00000000971       0       0     0
ENSG00000001461       0       0     0
ENSG00000004455       1       1     0
ENSG00000004487       0       0     1
ENSG00000007923       0       0     0
689 more rows ...

$[   0.362,   2.628)
                Method1 Method2 truth
ENSG00000007933       0       0     0
ENSG00000007968       1       1     0
ENSG00000009724       0       0     0
ENSG00000010932       0       0     1
ENSG00000024526       1       1     1
688 more rows ...

$overall
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000000971       0       0     0
ENSG00000001460       0       0     1
3853 more rows ...


@corr
data frame with 0 columns and 0 rows

@maxsplit
[1] 4

@splv
[1] "expr_cat"

@onlyshared
[1] FALSE

== testthat results  ===========================================================
[ OK: 382 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  49.28    0.43   51.17

iCOBRA.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(iCOBRA)
> 
> test_check("iCOBRA")
An object of class "COBRAData"
@pval
                   Method1     Method2     Method3
ENSG00000000457 0.01446441 0.008665558 0.003317162
ENSG00000000460 0.95247473 0.927616428 0.974301159
ENSG00000000938 0.74556923 0.632987431 0.639716304
ENSG00000000971 0.72582371 0.568683774 0.610769221
ENSG00000001460 0.64292689 0.629807292 0.613039563
2413 more rows ...

@padj
                   Method1    Method2
ENSG00000000457 0.05544853 0.03916508
ENSG00000000460 0.98752284 0.96680023
ENSG00000000938 0.91465571 0.82867282
ENSG00000000971 0.90618247 0.79410144
ENSG00000001460 0.87662457 0.82779499
2413 more rows ...

@sval
                   Method1    Method2
ENSG00000000457 0.05544853 0.03916508
ENSG00000000460 0.98752284 0.96680023
ENSG00000000938 0.91465571 0.82867282
ENSG00000000971 0.90618247 0.79410144
ENSG00000001460 0.87662457 0.82779499
2413 more rows ...

@score
                    Method1     Method2      Method3
ENSG00000000457 -0.76274305 -0.75783824 -0.743951068
ENSG00000000460 -0.02033394 -0.02096682 -0.007355491
ENSG00000000938  0.10235482  0.10968180  0.113127202
ENSG00000000971 -0.12495998 -0.12090589 -0.112072431
ENSG00000001460 -0.16319682 -0.13257307 -0.149343205
2413 more rows ...

@truth
                status n_isoforms      logFC     logFC_cat       expr
ENSG00000000457      0          5  0.0000000 [ 0.00, 0.56)   8.525774
ENSG00000000460      1         10  1.1643146 [ 0.56, 1.54)   5.371661
ENSG00000000938      0          8  0.0000000 [ 0.00, 0.56)  11.543626
ENSG00000000971      0          6  0.0000000 [ 0.00, 0.56) 163.547797
ENSG00000001460      1         13 -0.1033807 [ 0.00, 0.56)   6.874695
                           expr_cat
ENSG00000000457 [   2.628,  17.148)
ENSG00000000460 [   2.628,  17.148)
ENSG00000000938 [   2.628,  17.148)
ENSG00000000971 [  17.148,3265.406]
ENSG00000001460 [   2.628,  17.148)
3853 more rows ...

An object of class "COBRAPerformance"
@fdrtpr
data frame with 0 columns and 0 rows

@fdrtprcurve
data frame with 0 columns and 0 rows

@fdrnbr
data frame with 0 columns and 0 rows

@fdrnbrcurve
data frame with 0 columns and 0 rows

@fsrnbr
data frame with 0 columns and 0 rows

@fsrnbrcurve
data frame with 0 columns and 0 rows

@deviation
data frame with 0 columns and 0 rows

@tpr
      thr  method basemethod   meas      fullmethod splitval NBR  TP  FP   TN
1 thr0.01 Method1    Method1 __padj Method1_overall  overall 508 387 121 1473
2 thr0.01 Method2    Method2 __padj Method2_overall  overall 392 308  84 1510
3 thr0.05 Method1    Method1 __padj Method1_overall  overall 620 448 172 1422
4 thr0.05 Method2    Method2 __padj Method2_overall  overall 565 406 159 1435
5  thr0.1 Method1    Method1 __padj Method1_overall  overall 697 478 219 1375
6  thr0.1 Method2    Method2 __padj Method2_overall  overall 651 448 203 1391
   FN TOT_CALLED DIFF NONDIFF       TPR
1 437       2418  842    3016 0.4596200
2 516       2418  842    3016 0.3657957
3 376       2418  842    3016 0.5320665
4 418       2418  842    3016 0.4821853
5 346       2418  842    3016 0.5676960
6 376       2418  842    3016 0.5320665

@fpr
data frame with 0 columns and 0 rows

@roc
data frame with 0 columns and 0 rows

@scatter
data frame with 0 columns and 0 rows

@fpc
data frame with 0 columns and 0 rows

@overlap
data frame with 0 columns and 0 rows

@corr
data frame with 0 columns and 0 rows

@maxsplit
[1] 3

@splv
[1] "none"

@onlyshared
[1] FALSE

An object of class "COBRAPerformance"
@fdrtpr
data frame with 0 columns and 0 rows

@fdrtprcurve
data frame with 0 columns and 0 rows

@fdrnbr
data frame with 0 columns and 0 rows

@fdrnbrcurve
data frame with 0 columns and 0 rows

@fsrnbr
data frame with 0 columns and 0 rows

@fsrnbrcurve
data frame with 0 columns and 0 rows

@deviation
data frame with 0 columns and 0 rows

@tpr
      thr  method basemethod   meas                           fullmethod
1 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.000,   0.362)
2 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.362,   2.628)
3 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   2.628,  17.148)
4 thr0.01 Method1    Method1 __padj Method1_expr_cat:[  17.148,3265.406]
5 thr0.01 Method1    Method1 __padj                      Method1_overall
                      splitval NBR  TP  FP   TN  FN TOT_CALLED DIFF NONDIFF
1 expr_cat:[   0.000,   0.362)  18  12   6  341  12        371   30    1747
2 expr_cat:[   0.362,   2.628) 112 100  12  374 175        661  287     406
3 expr_cat:[   2.628,  17.148) 157 102  55  414 121        692  223     471
4 expr_cat:[  17.148,3265.406] 221 173  48  344 129        694  302     392
5                      overall 508 387 121 1473 437       2418  842    3016
        TPR
1 0.4000000
2 0.3484321
3 0.4573991
4 0.5728477
5 0.4596200
25 more rows ...

@fpr
data frame with 0 columns and 0 rows

@roc
data frame with 0 columns and 0 rows

@scatter
data frame with 0 columns and 0 rows

@fpc
data frame with 0 columns and 0 rows

@overlap
$[   0.000,   0.362)
                Method1 Method2 truth
ENSG00000007908       0       0     0
ENSG00000008118       0       0     0
ENSG00000042781       0       0     0
ENSG00000049247       0       0     1
ENSG00000057468       0       0     0
1772 more rows ...

$[   2.628,  17.148)
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000001460       0       0     1
ENSG00000006555       0       0     1
689 more rows ...

$[  17.148,3265.406]
                Method1 Method2 truth
ENSG00000000971       0       0     0
ENSG00000001461       0       0     0
ENSG00000004455       1       1     0
ENSG00000004487       0       0     1
ENSG00000007923       0       0     0
689 more rows ...

$[   0.362,   2.628)
                Method1 Method2 truth
ENSG00000007933       0       0     0
ENSG00000007968       1       1     0
ENSG00000009724       0       0     0
ENSG00000010932       0       0     1
ENSG00000024526       1       1     1
688 more rows ...

$overall
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000000971       0       0     0
ENSG00000001460       0       0     1
3853 more rows ...


@corr
data frame with 0 columns and 0 rows

@maxsplit
[1] 4

@splv
[1] "expr_cat"

@onlyshared
[1] FALSE

An object of class "COBRAPlot"
@plotcolors
                             Method1                              Method2 
                           "#00ACFC"                            "#8B93FF" 
                               truth Method1_expr_cat:[   0.000,   0.362) 
                           "#FF65AC"                            "#F8766D" 
Method2_expr_cat:[   0.000,   0.362) 
                           "#E18A00" 
58 more elements ...

@facetted
[1] FALSE

@fdrtpr
data frame with 0 columns and 0 rows

@fdrtprcurve
data frame with 0 columns and 0 rows

@fdrnbr
data frame with 0 columns and 0 rows

@fdrnbrcurve
data frame with 0 columns and 0 rows

@fsrnbr
data frame with 0 columns and 0 rows

@fsrnbrcurve
data frame with 0 columns and 0 rows

@deviation
data frame with 0 columns and 0 rows

@tpr
      thr  method basemethod   meas                           fullmethod
1 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.000,   0.362)
2 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   0.362,   2.628)
3 thr0.01 Method1    Method1 __padj Method1_expr_cat:[   2.628,  17.148)
4 thr0.01 Method1    Method1 __padj Method1_expr_cat:[  17.148,3265.406]
5 thr0.01 Method1    Method1 __padj                      Method1_overall
                      splitval NBR  TP  FP   TN  FN TOT_CALLED DIFF NONDIFF
1 expr_cat:[   0.000,   0.362)  18  12   6  341  12        371   30    1747
2 expr_cat:[   0.362,   2.628) 112 100  12  374 175        661  287     406
3 expr_cat:[   2.628,  17.148) 157 102  55  414 121        692  223     471
4 expr_cat:[  17.148,3265.406] 221 173  48  344 129        694  302     392
5                      overall 508 387 121 1473 437       2418  842    3016
        TPR num_method
1 0.4000000          1
2 0.3484321          2
3 0.4573991          3
4 0.5728477          4
5 0.4596200          5
25 more rows ...

@fpr
data frame with 0 columns and 0 rows

@roc
data frame with 0 columns and 0 rows

@scatter
data frame with 0 columns and 0 rows

@fpc
data frame with 0 columns and 0 rows

@overlap
$[   0.000,   0.362)
                Method1 Method2 truth
ENSG00000007908       0       0     0
ENSG00000008118       0       0     0
ENSG00000042781       0       0     0
ENSG00000049247       0       0     1
ENSG00000057468       0       0     0
1772 more rows ...

$[   2.628,  17.148)
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000001460       0       0     1
ENSG00000006555       0       0     1
689 more rows ...

$[  17.148,3265.406]
                Method1 Method2 truth
ENSG00000000971       0       0     0
ENSG00000001461       0       0     0
ENSG00000004455       1       1     0
ENSG00000004487       0       0     1
ENSG00000007923       0       0     0
689 more rows ...

$[   0.362,   2.628)
                Method1 Method2 truth
ENSG00000007933       0       0     0
ENSG00000007968       1       1     0
ENSG00000009724       0       0     0
ENSG00000010932       0       0     1
ENSG00000024526       1       1     1
688 more rows ...

$overall
                Method1 Method2 truth
ENSG00000000457       0       1     0
ENSG00000000460       0       0     1
ENSG00000000938       0       0     0
ENSG00000000971       0       0     0
ENSG00000001460       0       0     1
3853 more rows ...


@corr
data frame with 0 columns and 0 rows

@maxsplit
[1] 4

@splv
[1] "expr_cat"

@onlyshared
[1] FALSE

== testthat results  ===========================================================
[ OK: 382 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  47.35    0.34   47.68

Example timings

iCOBRA.Rcheck/examples_i386/iCOBRA-Ex.timings

nameusersystemelapsed
COBRAData0.020.000.02
COBRAPerformance000
COBRAPlot000
COBRAapp000
Extract0.250.000.25
basemethods0.230.020.25
calculate_adjp0.020.000.02
calculate_performance0.560.010.57
coerce0.10.00.1
corr0.030.000.03
deviation0.360.000.36
facetted0.070.000.08
fdrnbr0.110.000.11
fdrnbrcurve0.430.000.42
fdrtpr0.100.000.11
fdrtprcurve0.300.000.29
fpc0.280.000.29
fpr0.070.000.06
fsrnbr0.060.000.06
fsrnbrcurve0.750.000.75
maxsplit0.260.000.27
onlyshared0.080.000.07
overlap0.000.020.02
padj0.020.000.02
plot_corr0.40.00.4
plot_deviation0.850.000.85
plot_fdrnbrcurve0.810.010.82
plot_fdrtprcurve0.640.020.66
plot_fpc0.440.020.45
plot_fpr0.230.000.24
plot_fsrnbrcurve0.990.031.01
plot_overlap0.040.000.05
plot_roc0.470.000.47
plot_scatter0.780.000.78
plot_tpr0.360.000.36
plot_upset1.140.001.14
plotcolors0.080.000.08
prepare_data_for_plot0.580.000.58
pval0.020.000.01
reorder_levels0.090.000.10
roc0.380.000.38
scatter0.420.000.42
score0.020.000.01
splv0.390.000.39
stratiflevels0.280.000.29
sval0.010.000.01
tpr0.080.000.08
truth0.020.000.01
update_cobradata000
update_cobraperformance0.060.000.07

iCOBRA.Rcheck/examples_x64/iCOBRA-Ex.timings

nameusersystemelapsed
COBRAData000
COBRAPerformance000
COBRAPlot000
COBRAapp000
Extract0.350.020.36
basemethods0.390.010.41
calculate_adjp0.030.000.03
calculate_performance0.860.000.86
coerce0.160.000.16
corr0.040.000.04
deviation0.550.000.55
facetted0.120.020.14
fdrnbr0.110.000.11
fdrnbrcurve0.460.010.47
fdrtpr0.140.000.14
fdrtprcurve0.420.000.42
fpc0.250.000.25
fpr0.060.000.06
fsrnbr0.050.020.07
fsrnbrcurve101
maxsplit0.340.000.34
onlyshared0.090.000.09
overlap0.020.000.02
padj000
plot_corr0.470.000.47
plot_deviation1.120.041.16
plot_fdrnbrcurve1.380.031.40
plot_fdrtprcurve0.870.010.89
plot_fpc0.470.020.49
plot_fpr0.330.000.33
plot_fsrnbrcurve1.260.011.28
plot_overlap0.050.000.04
plot_roc0.690.000.69
plot_scatter1.080.001.07
plot_tpr0.390.020.41
plot_upset2.170.002.17
plotcolors0.110.000.11
prepare_data_for_plot0.780.000.78
pval0.020.000.02
reorder_levels0.110.000.11
roc0.390.000.39
scatter0.590.010.61
score0.020.000.01
splv0.340.000.35
stratiflevels0.280.020.29
sval000
tpr0.080.000.08
truth0.020.000.02
update_cobradata000
update_cobraperformance0.050.000.05