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CHECK report for iCOBRA on merida1

This page was generated on 2020-04-15 12:42:47 -0400 (Wed, 15 Apr 2020).

Package 822/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCOBRA 1.14.0
Charlotte Soneson
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/iCOBRA
Branch: RELEASE_3_10
Last Commit: 2d2d57a
Last Changed Date: 2019-10-29 13:09:30 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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: iCOBRA
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iCOBRA_1.14.0.tar.gz
StartedAt: 2020-04-15 03:07:09 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:09:52 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 162.8 seconds
RetCode: 0
Status:  OK 
CheckDir: iCOBRA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iCOBRA_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/iCOBRA.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iCOBRA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iCOBRA’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL iCOBRA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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
** 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
* DONE (iCOBRA)

Tests output

iCOBRA.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 69.681   1.404  71.601

Example timings

iCOBRA.Rcheck/iCOBRA-Ex.timings

nameusersystemelapsed
COBRAData0.0080.0010.009
COBRAPerformance0.0100.0000.011
COBRAPlot0.0030.0000.003
COBRAapp0.0030.0010.004
Extract0.3500.0160.370
basemethods0.5230.0180.543
calculate_adjp0.0220.0020.025
calculate_performance1.1830.0221.211
coerce0.1520.0070.158
corr0.0320.0030.034
deviation0.8950.0060.905
facetted0.1120.0050.119
fdrnbr0.1160.0050.121
fdrnbrcurve0.6280.0090.639
fdrtpr0.1200.0050.126
fdrtprcurve0.7010.0090.717
fpc0.4790.0100.492
fpr0.0970.0080.106
fsrnbr0.0610.0020.062
fsrnbrcurve0.9470.1561.109
maxsplit0.2450.0060.252
onlyshared0.0890.0020.092
overlap0.0130.0010.015
padj0.0070.0010.008
plot_corr0.5150.0130.531
plot_deviation1.3270.0131.350
plot_fdrnbrcurve1.0760.0071.089
plot_fdrtprcurve1.1290.0051.140
plot_fpc0.8070.0070.816
plot_fpr0.4160.0030.427
plot_fsrnbrcurve1.4290.1241.560
plot_overlap0.0380.0010.038
plot_roc0.8600.0040.866
plot_scatter1.3190.0101.335
plot_tpr0.4170.0040.424
plot_upset1.9190.0101.938
plotcolors0.0880.0020.090
prepare_data_for_plot1.1050.0131.125
pval0.0070.0010.008
reorder_levels0.0930.0060.098
roc0.4600.0020.461
scatter0.7570.0020.760
score0.0210.0010.022
splv0.2230.0010.230
stratiflevels0.2580.0060.263
sval0.0070.0010.007
tpr0.0670.0020.070
truth0.0100.0010.012
update_cobradata0.0020.0010.002
update_cobraperformance0.0760.0040.080