Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-06 11:10:10 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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

CHECK results for randRotation on merida1


To the developers/maintainers of the randRotation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/randRotation.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1576/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
randRotation 1.11.0  (landing page)
Peter Hettegger
Snapshot Date: 2022-12-05 14:00:11 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/randRotation
git_branch: master
git_last_commit: 594b5e0
git_last_commit_date: 2022-11-01 11:21:54 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: randRotation
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:randRotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings randRotation_1.11.0.tar.gz
StartedAt: 2022-12-06 05:06:50 -0500 (Tue, 06 Dec 2022)
EndedAt: 2022-12-06 05:08:40 -0500 (Tue, 06 Dec 2022)
EllapsedTime: 109.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: randRotation.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:randRotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings randRotation_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/randRotation.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘randRotation/DESCRIPTION’ ... OK
* this is package ‘randRotation’ version ‘1.11.0’
* 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 ‘randRotation’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
pFdr 15.085  0.488  20.012
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  sort(pFdr(res1, "fdr.qu"))[1:10] not equal to c(...).
  9/10 mismatches (average diff: 0.0496)
  [1] 0.870 - 0.470 ==  4.00e-01
  [2] 0.940 - 0.960 == -2.00e-02
  [3] 0.993 - 0.972 ==  2.14e-02
  [4] 0.998 - 0.994 ==  4.80e-03
  [5] 1.000 - 1.000 ==  2.31e-04
  [6] 1.000 - 1.000 == -7.13e-07
  [7] 1.000 - 1.000 ==  4.54e-06
  [8] 1.000 - 1.000 ==  1.36e-06
  [9] 1.000 - 1.000 == -1.20e-07
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]
  Error: Test failures
  Execution halted
* 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/randRotation.Rcheck/00check.log’
for details.


Installation output

randRotation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL randRotation
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘randRotation’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: randRotation
*** 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 (randRotation)

Tests output

randRotation.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(randRotation)
> 
> test_check("randRotation")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_rotateStat_pFdr.R:32'): Test execution of rotateStat (including parallel computation mode), pFdr with "fdr.q" and "fdr.qu" ──
sort(pFdr(res1))[1:10] not equal to c(...).
10/10 mismatches (average diff: 0.00198)
[1] 0.0088 - 0.0048 ==  0.0040
[2] 0.0095 - 0.0097 == -0.0002
[3] 0.0151 - 0.0144 ==  0.0007
[4] 0.0197 - 0.0199 == -0.0002
[5] 0.0259 - 0.0287 == -0.0028
[6] 0.0268 - 0.0294 == -0.0026
[7] 0.0362 - 0.0325 ==  0.0037
[8] 0.0394 - 0.0367 ==  0.0027
[9] 0.0457 - 0.0430 ==  0.0027
...
── Failure ('test_rotateStat_pFdr.R:33'): Test execution of rotateStat (including parallel computation mode), pFdr with "fdr.q" and "fdr.qu" ──
sort(pFdr(res1, "fdr.q"))[1:10] not equal to c(...).
9/10 mismatches (average diff: 0.0496)
[1] 0.870 - 0.470 ==  4.00e-01
[2] 0.940 - 0.960 == -2.00e-02
[3] 0.993 - 0.972 ==  2.14e-02
[4] 0.998 - 0.994 ==  4.80e-03
[5] 1.000 - 1.000 ==  2.31e-04
[6] 1.000 - 1.000 == -7.13e-07
[7] 1.000 - 1.000 ==  4.54e-06
[8] 1.000 - 1.000 ==  1.36e-06
[9] 1.000 - 1.000 == -1.20e-07
── Failure ('test_rotateStat_pFdr.R:34'): Test execution of rotateStat (including parallel computation mode), pFdr with "fdr.q" and "fdr.qu" ──
sort(pFdr(res1, "fdr.qu"))[1:10] not equal to c(...).
9/10 mismatches (average diff: 0.0496)
[1] 0.870 - 0.470 ==  4.00e-01
[2] 0.940 - 0.960 == -2.00e-02
[3] 0.993 - 0.972 ==  2.14e-02
[4] 0.998 - 0.994 ==  4.80e-03
[5] 1.000 - 1.000 ==  2.31e-04
[6] 1.000 - 1.000 == -7.13e-07
[7] 1.000 - 1.000 ==  4.54e-06
[8] 1.000 - 1.000 ==  1.36e-06
[9] 1.000 - 1.000 == -1.20e-07

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted

Example timings

randRotation.Rcheck/randRotation-Ex.timings

nameusersystemelapsed
X_decomp0.0020.0000.003
contrastModel0.0070.0000.013
initRandrot0.0210.0010.031
initRandrotW0.0420.0010.058
pFdr15.085 0.48820.012
qqunif0.0300.0010.045
randorth0.1290.0050.186
randpermut0.0000.0010.001
randrot0.0190.0030.032
rotateStat0.6380.0160.881
weights0.0190.0010.030