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This page was generated on 2023-07-08 11:37:48 -0400 (Sat, 08 Jul 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4610
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4344
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4350
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (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 359/2211HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clonality 1.49.0  (landing page)
Irina Ostrovnaya
Snapshot Date: 2023-07-07 14:05:07 -0400 (Fri, 07 Jul 2023)
git_url: https://git.bioconductor.org/packages/Clonality
git_branch: devel
git_last_commit: 0b0f24d
git_last_commit_date: 2023-04-25 10:18:35 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for Clonality on lconway


The builds on kunpeng2 (Linux ARM64) are experimental!
To the developers/maintainers of the Clonality package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Clonality.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.

raw results


Summary

Package: Clonality
Version: 1.49.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Clonality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Clonality_1.49.0.tar.gz
StartedAt: 2023-07-07 19:48:07 -0400 (Fri, 07 Jul 2023)
EndedAt: 2023-07-07 19:48:57 -0400 (Fri, 07 Jul 2023)
EllapsedTime: 50.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Clonality.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Clonality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Clonality_1.49.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Clonality.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* 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 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Clonality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Clonality’ version ‘1.49.0’
* 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 ‘Clonality’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
get.mutation.frequencies: no visible binding for global variable
  ‘freqdata’
Undefined global functions or variables:
  freqdata
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Clonality-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ECMtesting
> ### Title: Clonality testing of >=3 tumors using Extended Concordant
> ###   Mutations (ECM) test based on LOH (Loss of Heterozygosity) profiles
> ### Aliases: ECMtesting
> 
> ### ** Examples
> 
> set.seed(25)
> LOHtable<-cbind(1:15,matrix(sample(c(0,1,2),15*12,replace=TRUE),ncol=12))
> ECMtesting(LOHtable,rep(1:3,each=4),noloh=0,loh1=1,loh2=2,Nsim=100)
Testing clonality for patient 1, Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Calls: ECMtesting ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame
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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/Clonality.Rcheck/00check.log’
for details.


Installation output

Clonality.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Clonality
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Clonality’ ...
** using staged installation
** R
** data
** 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 (Clonality)

Tests output


Example timings

Clonality.Rcheck/Clonality-Ex.timings

nameusersystemelapsed