Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 972/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iCOBRA 1.28.1  (landing page)
Charlotte Soneson
Snapshot Date: 2023-10-15 14:00:07 -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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for iCOBRA on kjohnson2


To the developers/maintainers of the iCOBRA package:
- 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.

raw results


Summary

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: 2023-10-18 01:24:56 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 01:28:43 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 227.7 seconds
RetCode: 0
Status:   OK  
CheckDir: iCOBRA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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-mac-arm64/meat/iCOBRA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* 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-mac-arm64/meat/iCOBRA.Rcheck/00check.log’
for details.



Installation output

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-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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 
 56.156   1.021  87.584 

Example timings

iCOBRA.Rcheck/iCOBRA-Ex.timings

nameusersystemelapsed
COBRAData0.0070.0010.012
COBRAPerformance0.0040.0010.008
COBRAPlot0.0020.0000.006
COBRAapp0.5110.0450.854
Extract0.2540.0230.425
basemethods0.2830.0070.434
calculate_adjp0.0180.0030.032
calculate_performance0.6190.0170.974
coerce0.1040.0070.173
corr0.0300.0030.049
deviation0.4090.0060.643
facetted0.0870.0030.141
fdrnbr0.0970.0030.156
fdrnbrcurve0.2850.0060.448
fdrtpr0.1010.0050.164
fdrtprcurve0.2860.0060.436
fpc0.2730.0050.415
fpr0.0710.0030.112
fsrnbr0.0440.0010.070
fsrnbrcurve0.8180.0461.314
maxsplit0.5760.0160.893
onlyshared0.0790.0020.120
overlap0.0150.0020.025
padj0.0090.0010.013
plot_corr0.4160.0110.644
plot_deviation1.0300.0251.597
plot_fdrnbrcurve1.0610.0171.664
plot_fdrtprcurve0.8670.0141.359
plot_fpc0.6240.0100.974
plot_fpr0.3300.0060.514
plot_fsrnbrcurve1.3590.0342.143
plot_overlap0.0420.0040.064
plot_roc0.620.010.97
plot_scatter0.9630.0211.510
plot_tpr0.6460.0111.005
plot_upset1.8190.0302.850
plotcolors0.0880.0030.138
prepare_data_for_plot0.6680.0091.039
pval0.0100.0020.015
reorder_levels0.0820.0030.130
roc0.2850.0050.446
scatter0.4130.0050.640
score0.0090.0010.016
splv0.3540.0090.557
stratiflevels0.4230.0110.661
sval0.0080.0010.015
tpr0.0720.0030.114
truth0.0090.0010.018
update_cobradata0.0020.0000.003
update_cobraperformance0.0730.0010.112