Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2025-02-06 11:43 -0500 (Thu, 06 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4444
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 2216/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twilight 1.83.5  (landing page)
Stefanie Senger
Snapshot Date: 2025-02-05 13:48 -0500 (Wed, 05 Feb 2025)
git_url: https://git.bioconductor.org/packages/twilight
git_branch: devel
git_last_commit: 286cff8
git_last_commit_date: 2025-02-03 18:35:46 -0500 (Mon, 03 Feb 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    TIMEOUT  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped


BUILD results for twilight on lconway

To the developers/maintainers of the twilight package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/twilight.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: twilight
Version: 1.83.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data twilight
StartedAt: 2025-02-05 18:38:40 -0500 (Wed, 05 Feb 2025)
EndedAt: 2025-02-05 18:38:54 -0500 (Wed, 05 Feb 2025)
EllapsedTime: 13.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data twilight
###
##############################################################################
##############################################################################


* checking for file ‘twilight/DESCRIPTION’ ... OK
* preparing ‘twilight’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘tr_2004_01.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

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


Error: processing vignette 'tr_2004_01.Rnw' failed with diagnostics:
 chunk 5 
Error in ns(l, df = 3) : could not find function "ns"

--- failed re-building ‘tr_2004_01.Rnw’

pdflatex tr_2004_01
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./tr_2004_01.tex
LaTeX2e <2021-11-15> patch level 1
L3 programming layer <2022-02-24>
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/report.cls
Document Class: report 2021/10/04 v1.4n Standard LaTeX document class
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/fleqn.clo)
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/size11.clo)) (./compdiag.sty
(/usr/local/texlive/2022/texmf-dist/tex/generic/iftex/ifpdf.sty
(/usr/local/texlive/2022/texmf-dist/tex/generic/iftex/iftex.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2022/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2022/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2022/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2022/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2022/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2022/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2022/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2022/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/local/texlive/2022/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2022/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2022/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2022/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty
))) (/usr/local/texlive/2022/texmf-dist/tex/latex/ntgclass/a4.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/local/texlive/2022/texmf-dist/tex/generic/iftex/ifvtex.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/tools/theorem.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/tools/thp.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/tools/thb.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/caption/caption.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/caption/caption3.sty))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Sweave.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/fontenc.sty))
(/usr/local/texlive/2022/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file tr_2004_01.aux.
(/usr/local/texlive/2022/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2022/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/grfext/grfext.sty)
(/usr/local/texlive/2022/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2022/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2022/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2022/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/t1cmss.fd)
(/usr/local/texlive/2022/texmf-dist/tex/latex/base/t1cmtt.fd) [1{/usr/local/tex
live/2022/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./bcb_logo.pdf> <./MPI
MG_logo.png>]
pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has 
been already used, duplicate ignored
<to be read again> 
                   \relax 
l.51 \chapter
             {Introduction} [1]
Chapter 1.

LaTeX Warning: Citation `scheid04' on page 2 undefined on input line 53.


LaTeX Warning: Citation `scheid05' on page 2 undefined on input line 53.


LaTeX Warning: Citation `scheid06' on page 2 undefined on input line 53.

[2]
Chapter 2.

Underfull \hbox (badness 10000) in paragraph at lines 73--73
[]\T1/cmtt/m/n/10.95 twilight.pval(xin, yin, method="fc", paired=FALSE, B=1000,
 yperm=NULL,

Overfull \hbox (0.52287pt too wide) in paragraph at lines 73--75
[]  

LaTeX Warning: Citation `tusher01' on page 3 undefined on input line 84.


LaTeX Warning: Citation `efron01' on page 3 undefined on input line 84.

[3]

LaTeX Warning: Citation `scheid04' on page 4 undefined on input line 94.


Overfull \hbox (31.82951pt too wide) in paragraph at lines 96--98
[]\T1/cmr/m/n/10.95 Function \T1/cmtt/m/n/10.95 twilight.pval \T1/cmr/m/n/10.95
 han-dles paired and un-paired data. In the un-paired case (\T1/cmtt/m/n/10.95 
paired=FALSE\T1/cmr/m/n/10.95 ),

LaTeX Warning: Citation `golub99' on page 4 undefined on input line 99.


LaTeX Warning: Citation `huber02' on page 4 undefined on input line 99.

[4]

LaTeX Warning: Reference `twilight.combi' on page 5 undefined on input line 128
.


LaTeX Warning: Citation `tusher01' on page 5 undefined on input line 130.

)
Runaway argument?
! File ended while scanning use of \FancyVerbGetLine.
<inserted text> 
                \par 
<*> tr_2004_01
              
? 
! Emergency stop.
<inserted text> 
                \par 
<*> tr_2004_01
              
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on tr_2004_01.log.
make: *** [vign] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted