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This page was generated on 2024-03-27 11:38:50 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 2140/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TnT 1.25.1  (landing page)
Jialin Ma
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/TnT
git_branch: devel
git_last_commit: 729c086
git_last_commit_date: 2024-02-29 13:05:00 -0400 (Thu, 29 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for TnT on palomino3


To the developers/maintainers of the TnT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TnT.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: TnT
Version: 1.25.1
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TnT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings TnT_1.25.1.tar.gz
StartedAt: 2024-03-27 07:18:49 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 07:20:46 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 117.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TnT.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TnT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings TnT_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/TnT.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TnT/DESCRIPTION' ... OK
* this is package 'TnT' version '1.25.1'
* 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 whether package 'TnT' 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 code 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 whether startup messages can be suppressed ... 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'TnT-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seqinfo
> ### Title: Seqinfo of TnTTrack and TnTBoard
> ### Aliases: seqinfo seqinfo<-,RangeBasedTrack-method
> ###   seqinfo,RangeBasedTrack-method seqlevelsInUse,RangeBasedTrack-method
> ###   seqinfo,TnTBoard-method seqinfo,CompositeTrack-method
> ###   seqinfo<-,CompositeTrack-method seqlevelsInUse,CompositeTrack-method
> 
> ### ** Examples
> 
> btrack1 <- BlockTrack(GRanges("chr1", IRanges(1, 123)))
> btrack2 <- BlockTrack(GRanges("chr2", IRanges(3, 599)))
> ctrack <- merge(btrack1, btrack2)
Warning in .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
Error in .mergeSpec(tracklist) : is.atomic(backgrounds) is not TRUE
Calls: merge ... merge_tracklist -> .merge_tracklist -> .mergeSpec -> stopifnot
Execution halted
* 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:
    1. ├─testthat::expect_warning(ct <- merge(bt, bt2), "no sequence levels in common") at test-seqinfo.R:17:5
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─base::merge(bt, bt2)
    7. └─TnT::merge(bt, bt2)
    8.   └─TnT:::merge_tracklist(tracklist)
    9.     └─TnT (local) .merge_tracklist(tracklist)
   10.       └─TnT (local) .mergeSpec(tracklist)
   11.         └─base::stopifnot(is.atomic(labels), is.atomic(heights), is.atomic(backgrounds))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 30 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/TnT.Rcheck/00check.log'
for details.


Installation output

TnT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL TnT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'TnT' ...
** 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
Warning in fun(libname, pkgname) :
  Package 'TnT' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'TnT' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (TnT)

Tests output

TnT.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(TnT)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Warning message:
In fun(libname, pkgname) :
  Package 'TnT' is deprecated and will be removed from Bioconductor
  version 3.20
> 
> test_check("TnT")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 30 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-seqinfo.R:17:5'): seqinfo of CompositeTrack ────────────────────
Error in `.mergeSpec(tracklist)`: is.atomic(backgrounds) is not TRUE
Backtrace:
     ▆
  1. ├─testthat::expect_warning(ct <- merge(bt, bt2), "no sequence levels in common") at test-seqinfo.R:17:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─base::merge(bt, bt2)
  7. └─TnT::merge(bt, bt2)
  8.   └─TnT:::merge_tracklist(tracklist)
  9.     └─TnT (local) .merge_tracklist(tracklist)
 10.       └─TnT (local) .mergeSpec(tracklist)
 11.         └─base::stopifnot(is.atomic(labels), is.atomic(heights), is.atomic(backgrounds))

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 30 ]
Error: Test failures
Execution halted

Example timings

TnT.Rcheck/TnT-Ex.timings

nameusersystemelapsed
TnT-shiny0.250.080.33
composite-track0.330.000.33
knit_print.TnTBoard0.070.000.06
mapcol000
saveTnT0.480.030.88