Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

This page was generated on 2023-10-20 09:38:09 -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 1610/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuartPAC 1.32.0  (landing page)
Gregory Ryslik
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/QuartPAC
git_branch: RELEASE_3_17
git_last_commit: 86b0f5f
git_last_commit_date: 2023-04-25 10:36:44 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for QuartPAC on kjohnson2


To the developers/maintainers of the QuartPAC 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: QuartPAC
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QuartPAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QuartPAC_1.32.0.tar.gz
StartedAt: 2023-10-18 17:00:27 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 17:06:09 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 341.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: QuartPAC.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QuartPAC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QuartPAC_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuartPAC.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 ‘QuartPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuartPAC’ version ‘1.32.0’
* 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 ‘QuartPAC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
alignPositions: no visible global function definition for
  ‘PhredQuality’
alignPositions: no visible global function definition for
  ‘pairwiseAlignment’
constructCanonicalNumbering: no visible global function definition for
  ‘pattern’
constructCanonicalNumbering: no visible global function definition for
  ‘subject’
constructCanonicalNumbering: no visible global function definition for
  ‘start’
getMutations : <anonymous>: no visible global function definition for
  ‘read.table’
getRangeLocInfo: no visible global function definition for ‘aggregate’
quartCluster: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  PhredQuality aggregate capture.output pairwiseAlignment pattern
  read.table start subject
Consider adding
  importFrom("stats", "aggregate", "start")
  importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
* 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
QuartPAC-package          32.077  0.543  61.600
makeAlignedSuperStructure 10.468  0.165  19.670
quartCluster              10.393  0.167  22.583
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  QuartPAC RUnit Tests - 1 test function, 0 errors, 1 failure
  FAILURE in test_quartCluster: Error in checkEquals(dim(quart_results$ipac)[1], 35) : 
    Mean relative difference: 0.02777778
  
  
  Test files with failing tests
  
     test_quartCluster.R 
       test_quartCluster 
  
  
  Error in BiocGenerics:::testPackage("QuartPAC") : 
    unit tests failed for package QuartPAC
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuartPAC.Rcheck/00check.log’
for details.


Installation output

QuartPAC.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘QuartPAC’ ...
** using staged installation
** R
** 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 (QuartPAC)

Tests output

QuartPAC.Rcheck/tests/runTests.Rout.fail


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.

> BiocGenerics:::testPackage("QuartPAC")

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith


Attaching package: 'BiocGenerics'

The following object is masked from 'package:gdata':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:gdata':

    first, first<-

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:gdata':

    trim


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'igraph'

The following object is masked from 'package:Biostrings':

    union

The following object is masked from 'package:XVector':

    path

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn


Attaching package: 'data.table'

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

The following objects are masked from 'package:gdata':

    first, last

Performing SpacePAC calculations
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.50 
Performing iPAC Calculations
[1] "Running Remapped"
Performing GraphPAC Calculations
Calculating Remapped Clusters.Timing stopped at: 24.95 0.436 44.41
Error in checkEquals(dim(quart_results$ipac)[1], 35) : 
  Mean relative difference: 0.02777778



RUNIT TEST PROTOCOL -- Wed Oct 18 17:05:56 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
QuartPAC RUnit Tests - 1 test function, 0 errors, 1 failure
FAILURE in test_quartCluster: Error in checkEquals(dim(quart_results$ipac)[1], 35) : 
  Mean relative difference: 0.02777778


Test files with failing tests

   test_quartCluster.R 
     test_quartCluster 


Error in BiocGenerics:::testPackage("QuartPAC") : 
  unit tests failed for package QuartPAC
Execution halted

Example timings

QuartPAC.Rcheck/QuartPAC-Ex.timings

nameusersystemelapsed
QuartPAC-package32.077 0.54361.600
getMutations0.0730.0223.020
makeAlignedSuperStructure10.468 0.16519.670
quartCluster10.393 0.16722.583