Charlotte Soneson
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/iCOBRA |
| git_branch: RELEASE_3_17 |
| git_last_commit: 3e6ad66 |
| git_last_commit_date: 2023-07-10 13:15:46 -0400 (Mon, 10 Jul 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:09 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 972/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iCOBRA 1.28.1 (landing page) Charlotte Soneson
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the iCOBRA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iCOBRA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: iCOBRA |
| Version: 1.28.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iCOBRA_1.28.1.tar.gz |
| StartedAt: 2023-10-16 02:48:14 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:53:52 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 338.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iCOBRA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iCOBRA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iCOBRA_1.28.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/iCOBRA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iCOBRA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iCOBRA’ version ‘1.28.1’
* 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 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 ... NOTE
Namespace in Imports field not imported from: ‘markdown’
All declared Imports should be used.
* 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 LazyData ... 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/iCOBRA.Rcheck/00check.log’
for details.
iCOBRA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL iCOBRA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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)
iCOBRA.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
[ FAIL 0 | WARN 118 | SKIP 0 | PASS 395 ]
[ FAIL 0 | WARN 118 | SKIP 0 | PASS 395 ]
>
> proc.time()
user system elapsed
114.949 1.520 147.405
iCOBRA.Rcheck/iCOBRA-Ex.timings
| name | user | system | elapsed | |
| COBRAData | 0.012 | 0.002 | 0.017 | |
| COBRAPerformance | 0.010 | 0.003 | 0.015 | |
| COBRAPlot | 0.003 | 0.001 | 0.004 | |
| COBRAapp | 0.786 | 0.069 | 1.092 | |
| Extract | 0.502 | 0.071 | 0.736 | |
| basemethods | 0.632 | 0.016 | 0.835 | |
| calculate_adjp | 0.027 | 0.005 | 0.040 | |
| calculate_performance | 1.320 | 0.025 | 1.780 | |
| coerce | 0.173 | 0.015 | 0.255 | |
| corr | 0.047 | 0.004 | 0.066 | |
| deviation | 0.947 | 0.009 | 1.269 | |
| facetted | 0.163 | 0.005 | 0.216 | |
| fdrnbr | 0.139 | 0.008 | 0.191 | |
| fdrnbrcurve | 0.641 | 0.011 | 0.860 | |
| fdrtpr | 0.145 | 0.008 | 0.194 | |
| fdrtprcurve | 0.623 | 0.015 | 0.829 | |
| fpc | 0.595 | 0.008 | 0.796 | |
| fpr | 0.125 | 0.005 | 0.178 | |
| fsrnbr | 0.085 | 0.003 | 0.110 | |
| fsrnbrcurve | 1.498 | 0.081 | 2.127 | |
| maxsplit | 1.029 | 0.019 | 1.401 | |
| onlyshared | 0.139 | 0.005 | 0.193 | |
| overlap | 0.037 | 0.003 | 0.047 | |
| padj | 0.013 | 0.003 | 0.017 | |
| plot_corr | 0.712 | 0.012 | 0.963 | |
| plot_deviation | 2.052 | 0.035 | 2.776 | |
| plot_fdrnbrcurve | 1.902 | 0.022 | 2.562 | |
| plot_fdrtprcurve | 1.696 | 0.015 | 2.232 | |
| plot_fpc | 1.245 | 0.011 | 1.636 | |
| plot_fpr | 0.624 | 0.007 | 0.836 | |
| plot_fsrnbrcurve | 2.321 | 0.042 | 3.483 | |
| plot_overlap | 0.067 | 0.004 | 0.109 | |
| plot_roc | 1.211 | 0.011 | 1.787 | |
| plot_scatter | 1.876 | 0.034 | 2.487 | |
| plot_tpr | 0.986 | 0.015 | 1.349 | |
| plot_upset | 3.292 | 0.032 | 4.520 | |
| plotcolors | 0.161 | 0.003 | 0.222 | |
| prepare_data_for_plot | 1.368 | 0.013 | 1.859 | |
| pval | 0.022 | 0.004 | 0.039 | |
| reorder_levels | 0.128 | 0.003 | 0.168 | |
| roc | 0.586 | 0.007 | 0.798 | |
| scatter | 0.946 | 0.009 | 1.354 | |
| score | 0.012 | 0.002 | 0.020 | |
| splv | 0.591 | 0.010 | 0.830 | |
| stratiflevels | 0.662 | 0.013 | 0.953 | |
| sval | 0.011 | 0.003 | 0.019 | |
| tpr | 0.120 | 0.004 | 0.161 | |
| truth | 0.014 | 0.003 | 0.031 | |
| update_cobradata | 0.003 | 0.000 | 0.005 | |
| update_cobraperformance | 0.102 | 0.001 | 0.129 | |