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This page was generated on 2023-05-26 06:18:03 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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BUILD results for aCGH on kunpeng2


To the developers/maintainers of the aCGH package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/aCGH.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 12/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aCGH 1.79.0  (landing page)
Peter Dimitrov
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/aCGH
git_branch: devel
git_last_commit: 1b45ed9
git_last_commit_date: 2023-04-25 13:40:31 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

Summary

Package: aCGH
Version: 1.79.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data aCGH
StartedAt: 2023-05-25 20:00:59 -0000 (Thu, 25 May 2023)
EndedAt: 2023-05-25 20:01:33 -0000 (Thu, 25 May 2023)
EllapsedTime: 34.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data aCGH
###
##############################################################################
##############################################################################


* checking for file ‘aCGH/DESCRIPTION’ ... OK
* preparing ‘aCGH’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘aCGH.Rnw’ using Sweave
Loading required package: cluster
Loading required package: survival
Loading required package: multtest
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: ‘aCGH’

The following object is masked from ‘package:stats’:

    heatmap

Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm) :
  collapsing to unique 'x' values
Warning in `[.aCGH`(colorectal, , 1:3) :
  subsetting the log2.ratios only
Warning in min(indstretch[indstretch > indaber[m]]) :
  no non-missing arguments to min; returning Inf
Warning in min(indstretch[indstretch > indaber[m]]) :
  no non-missing arguments to min; returning Inf
Warning in min(indstretch[indstretch > indaber[m]]) :
  no non-missing arguments to min; returning Inf
Warning in max(indstretch[indstretch < indaber[m]]) :
  no non-missing arguments to max; returning -Inf
Warning in min(indstretch[indstretch > indaber[m]]) :
  no non-missing arguments to min; returning Inf
Warning in min(indstretch[indstretch > indaber[m]]) :
  no non-missing arguments to min; returning Inf
Warning in min(indstretch[indstretch > indaber[m]]) :
  no non-missing arguments to min; returning Inf
Warning in min(indstretch[indstretch > indaber[m]]) :
  no non-missing arguments to min; returning Inf
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in (function (z, notch = FALSE, width = NULL, varwidth = FALSE,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
Warning in `[.aCGH`(colorectal, , age.na) :
  subsetting the log2.ratios only
Warning in `[.aCGH`(aCGH.obj, , !is.na(response)) :
  subsetting the log2.ratios only
Warning in `[.aCGH`(aCGH.obj, , !is.na(response)) :
  subsetting the log2.ratios only
Error: processing vignette 'aCGH.Rnw' failed with diagnostics:
unable to run pdflatex on 'aCGH.tex'
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.17 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘aCGH.Rnw’

SUMMARY: processing the following file failed:
  ‘aCGH.Rnw’

Error: Vignette re-building failed.
Execution halted