Multiple platform build/check report for BioC 3.21 - BUILD results for pcaMethods on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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*

BUILD results for pcaMethods on palomino7

To the developers/maintainers of the pcaMethods package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pcaMethods.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: pcaMethods

Version: 2.0.0

Command: chmod a+r pcaMethods -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pcaMethods

StartedAt: 2025-04-17 21:16:46 -0400 (Thu, 17 Apr 2025)

EndedAt: 2025-04-17 21:19:15 -0400 (Thu, 17 Apr 2025)

EllapsedTime: 148.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r pcaMethods -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pcaMethods
###
##############################################################################
##############################################################################


* checking for file 'pcaMethods/DESCRIPTION' ... OK
* preparing 'pcaMethods':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'missingValues.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")'.


Attaching package: 'pcaMethods'

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

    loadings

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "missingValues.tex" ' had status 1033
Error: processing vignette 'missingValues.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'missingValues.pdf' for vignette with name 'missingValues' and engine 'utils::Sweave'. The following files exist in working directory 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4GGKC4\Rbuild11f5839b5bbe\pcaMethods\vignettes': 'missingValues.Rnw' (2988 bytes), 'missingValues.tex' (3601 bytes), 'outliers.Rnw' (5145 bytes), 'pcaMethods.Rnw' (23394 bytes)
--- failed re-building 'missingValues.Rnw'

--- re-building 'outliers.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "outliers.tex" ' had status 1033
Error: processing vignette 'outliers.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'outliers.pdf' for vignette with name 'outliers' and engine 'utils::Sweave'. The following files exist in working directory 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp4GGKC4\Rbuild11f5839b5bbe\pcaMethods\vignettes': 'missingValues.R' (1776 bytes), 'missingValues.Rnw' (2988 bytes), 'missingValues.tex' (3601 bytes), 'outliers-005.pdf' (16974 bytes), 'outliers.Rnw' (5145 bytes), 'outliers.tex' (4931 bytes), 'pcaMethods.Rnw' (23394 bytes)
--- failed re-building 'outliers.Rnw'

--- re-building 'pcaMethods.Rnw' using Sweave
--- finished re-building 'pcaMethods.Rnw'

SUMMARY: processing the following files failed:
  'missingValues.Rnw' 'outliers.Rnw'

Error: Vignette re-building failed.
Execution halted