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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:57 -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 853/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iCOBRA 1.16.0 Charlotte Soneson
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: iCOBRA |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings iCOBRA_1.16.0.tar.gz |
| StartedAt: 2020-10-17 02:17:14 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:19:17 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 122.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iCOBRA.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings iCOBRA_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/iCOBRA.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’ * 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 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
iCOBRA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL iCOBRA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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)
iCOBRA.Rcheck/tests/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-pc-linux-gnu (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
44.033 0.187 44.546
iCOBRA.Rcheck/iCOBRA-Ex.timings
| name | user | system | elapsed | |
| COBRAData | 0.01 | 0.00 | 0.01 | |
| COBRAPerformance | 0.008 | 0.000 | 0.009 | |
| COBRAPlot | 0.003 | 0.000 | 0.003 | |
| COBRAapp | 0.003 | 0.000 | 0.003 | |
| Extract | 0.394 | 0.004 | 0.399 | |
| basemethods | 0.413 | 0.004 | 0.417 | |
| calculate_adjp | 0.022 | 0.000 | 0.022 | |
| calculate_performance | 0.595 | 0.003 | 0.598 | |
| coerce | 0.092 | 0.000 | 0.091 | |
| corr | 0.025 | 0.000 | 0.024 | |
| deviation | 0.325 | 0.000 | 0.324 | |
| facetted | 0.079 | 0.000 | 0.079 | |
| fdrnbr | 0.084 | 0.000 | 0.083 | |
| fdrnbrcurve | 0.245 | 0.004 | 0.249 | |
| fdrtpr | 0.073 | 0.004 | 0.076 | |
| fdrtprcurve | 0.241 | 0.000 | 0.241 | |
| fpc | 0.218 | 0.000 | 0.219 | |
| fpr | 0.068 | 0.004 | 0.072 | |
| fsrnbr | 0.047 | 0.000 | 0.047 | |
| fsrnbrcurve | 0.604 | 0.008 | 0.612 | |
| maxsplit | 0.258 | 0.000 | 0.258 | |
| onlyshared | 0.073 | 0.000 | 0.073 | |
| overlap | 0.011 | 0.000 | 0.012 | |
| padj | 0.007 | 0.000 | 0.007 | |
| plot_corr | 0.380 | 0.000 | 0.381 | |
| plot_deviation | 0.900 | 0.020 | 0.921 | |
| plot_fdrnbrcurve | 0.820 | 0.016 | 0.836 | |
| plot_fdrtprcurve | 1.041 | 0.000 | 1.041 | |
| plot_fpc | 0.61 | 0.00 | 0.61 | |
| plot_fpr | 0.253 | 0.000 | 0.253 | |
| plot_fsrnbrcurve | 1.007 | 0.000 | 1.007 | |
| plot_overlap | 0.062 | 0.000 | 0.063 | |
| plot_roc | 0.79 | 0.00 | 0.79 | |
| plot_scatter | 1.042 | 0.004 | 1.046 | |
| plot_tpr | 0.361 | 0.000 | 0.361 | |
| plot_upset | 1.208 | 0.004 | 1.212 | |
| plotcolors | 0.081 | 0.000 | 0.081 | |
| prepare_data_for_plot | 0.543 | 0.004 | 0.547 | |
| pval | 0.007 | 0.000 | 0.007 | |
| reorder_levels | 0.079 | 0.000 | 0.080 | |
| roc | 0.237 | 0.000 | 0.237 | |
| scatter | 0.343 | 0.004 | 0.347 | |
| score | 0.007 | 0.000 | 0.007 | |
| splv | 0.227 | 0.000 | 0.226 | |
| stratiflevels | 0.283 | 0.000 | 0.283 | |
| sval | 0.007 | 0.000 | 0.007 | |
| tpr | 0.072 | 0.000 | 0.072 | |
| truth | 0.009 | 0.000 | 0.008 | |
| update_cobradata | 0.003 | 0.000 | 0.002 | |
| update_cobraperformance | 0.057 | 0.000 | 0.057 | |