Back to "Blame Jeroen" build/check report for BioC 3.11

BUILD report for snpStats on tokay2

This page was generated on 2020-04-15 03:20:11 -0400 (Wed, 15 Apr 2020).

These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html)
TO THE DEVELOPERS/MAINTAINERS OF THE snpStats PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 79/89HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snpStats 1.37.0
David Clayton
Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/snpStats
Branch: master
Last Commit: 18599d4
Last Changed Date: 2019-10-29 13:34:48 -0400 (Tue, 29 Oct 2019)
tokay2 Windows Server 2012 R2 Standard / x64  OK [ ERROR ] skipped  skipped 

Summary

Package: snpStats
Version: 1.37.0
Command: chmod a+r snpStats -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data snpStats
StartedAt: 2020-04-14 19:08:19 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:10:58 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 158.8 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r snpStats -R && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data snpStats
###
##############################################################################
##############################################################################


* checking for file 'snpStats/DESCRIPTION' ... OK
* preparing 'snpStats':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building 'Fst-vignette.Rnw' using Sweave
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "Fst-vignette.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'Fst-vignette.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'Fst-vignette.pdf' for vignette with name 'Fst-vignette' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'differences.Rnw' (5962 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'index.html' (2023 bytes), 'ld-vignette.Rnw' (12641 bytes), 'pca-vignette.Rnw' (9345 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'tdt-vignette.Rnw' (5171 bytes)
--- failed re-building 'Fst-vignette.Rnw'

--- re-building 'data-input-vignette.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "data-input-vignette.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'data-input-vignette.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'data-input-vignette.pdf' for vignette with name 'data-input-vignette' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.R' (885 bytes), 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'data-input-vignette.tex' (20652 bytes), 'differences.Rnw' (5962 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'index.html' (2023 bytes), 'ld-vignette.Rnw' (12641 bytes), 'pca-vignette.Rnw' (9345 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'tdt-vignette.Rnw' (5171 bytes)
--- failed re-building 'data-input-vignette.Rnw'

--- re-building 'differences.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "differences.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'differences.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'differences.pdf' for vignette with name 'differences' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.R' (885 bytes), 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.R' (3287 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'data-input-vignette.tex' (20652 bytes), 'differences.Rnw' (5962 bytes), 'differences.tex' (6059 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'index.html' (2023 bytes), 'ld-vignette.Rnw' (12641 bytes), 'pca-vignette.Rnw' (9345 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'tdt-vignette.Rnw' (5171 bytes)
--- failed re-building 'differences.Rnw'

--- re-building 'imputation-vignette.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "imputation-vignette.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'imputation-vignette.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'imputation-vignette.pdf' for vignette with name 'imputation-vignette' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.R' (885 bytes), 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.R' (3287 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'data-input-vignette.tex' (20652 bytes), 'differences.R' (53 bytes), 'differences.Rnw' (5962 bytes), 'differences.tex' (6059 bytes), 'imputation-vignette-best.pdf' (12365 bytes), 'imputation-vignette-compare.pdf' (15901 bytes), 'imputation-vignette-imptest-rhs.pdf' (15894 bytes), 'imputation-vignette-mach.pdf' (5362 bytes), 'imputation-vignette-rsqmaf.pdf' (36322 bytes), 'imputation-vignette-ruleplot.pdf' (4784 bytes), 'imputation-vignette-uncert1.pdf' (4685 bytes), 'imputation-vignette-uncert2.pdf' (4783 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'imputation-vignette.tex' (23171 bytes), 'index.html' (2023 bytes), 'ld-vignette.Rnw' (12641 bytes), 'pca-vignette.Rnw' (9345 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'tdt-vignette.Rnw' (5171 bytes)
--- failed re-building 'imputation-vignette.Rnw'

--- re-building 'ld-vignette.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "ld-vignette.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'ld-vignette.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'ld-vignette.pdf' for vignette with name 'ld-vignette' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.R' (885 bytes), 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.R' (3287 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'data-input-vignette.tex' (20652 bytes), 'differences.R' (53 bytes), 'differences.Rnw' (5962 bytes), 'differences.tex' (6059 bytes), 'imputation-vignette-best.pdf' (12365 bytes), 'imputation-vignette-compare.pdf' (15901 bytes), 'imputation-vignette-imptest-rhs.pdf' (15894 bytes), 'imputation-vignette-mach.pdf' (5362 bytes), 'imputation-vignette-rsqmaf.pdf' (36322 bytes), 'imputation-vignette-ruleplot.pdf' (4784 bytes), 'imputation-vignette-uncert1.pdf' (4685 bytes), 'imputation-vignette-uncert2.pdf' (4783 bytes), 'imputation-vignette.R' (6625 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'imputation-vignette.tex' (23171 bytes), 'index.html' (2023 bytes), 'ld-vignette-clplot.pdf' (6316 bytes), 'ld-vignette-dpplot1.pdf' (7340 bytes), 'ld-vignette-dpplot2.pdf' (6332 bytes), 'ld-vignette-drplot.pdf' (12831 bytes), 'ld-vignette-eplot.pdf' (16096 bytes), 'ld-vignette-image1a.pdf' (232994 bytes), 'ld-vignette-image2a.pdf' (239457 bytes), 'ld-vignette-image3a.pdf' (66745 bytes), 'ld-vignette-image4a.pdf' (60700 bytes), 'ld-vignette-imagecola.pdf' (224839 bytes), 'ld-vignette.Rnw' (12641 bytes), 'ld-vignette.tex' (15175 bytes), 'pca-vignette.Rnw' (9345 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'tdt-vignette.Rnw' (5171 bytes)
--- failed re-building 'ld-vignette.Rnw'

--- re-building 'pca-vignette.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "pca-vignette.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'pca-vignette.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'pca-vignette.pdf' for vignette with name 'pca-vignette' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.R' (885 bytes), 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.R' (3287 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'data-input-vignette.tex' (20652 bytes), 'differences.R' (53 bytes), 'differences.Rnw' (5962 bytes), 'differences.tex' (6059 bytes), 'imputation-vignette-best.pdf' (12365 bytes), 'imputation-vignette-compare.pdf' (15901 bytes), 'imputation-vignette-imptest-rhs.pdf' (15894 bytes), 'imputation-vignette-mach.pdf' (5362 bytes), 'imputation-vignette-rsqmaf.pdf' (36322 bytes), 'imputation-vignette-ruleplot.pdf' (4784 bytes), 'imputation-vignette-uncert1.pdf' (4685 bytes), 'imputation-vignette-uncert2.pdf' (4783 bytes), 'imputation-vignette.R' (6625 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'imputation-vignette.tex' (23171 bytes), 'index.html' (2023 bytes), 'ld-vignette-clplot.pdf' (6316 bytes), 'ld-vignette-dpplot1.pdf' (7340 bytes), 'ld-vignette-dpplot2.pdf' (6332 bytes), 'ld-vignette-drplot.pdf' (12831 bytes), 'ld-vignette-eplot.pdf' (16096 bytes), 'ld-vignette-image1a.pdf' (232994 bytes), 'ld-vignette-image2a.pdf' (239457 bytes), 'ld-vignette-image3a.pdf' (66745 bytes), 'ld-vignette-image4a.pdf' (60700 bytes), 'ld-vignette-imagecola.pdf' (224839 bytes), 'ld-vignette.R' (7240 bytes), 'ld-vignette.Rnw' (12641 bytes), 'ld-vignette.tex' (15175 bytes), 'pca-vignette-pc-one.pdf' (5944 bytes), 'pca-vignette-testing.pdf' (146512 bytes), 'pca-vignette.Rnw' (9345 bytes), 'pca-vignette.tex' (10194 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'tdt-vignette.Rnw' (5171 bytes)
--- failed re-building 'pca-vignette.Rnw'

--- re-building 'snpStats-vignette.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "snpStats-vignette.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'snpStats-vignette.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'snpStats-vignette.pdf' for vignette with name 'snpStats-vignette' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.R' (885 bytes), 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.R' (3287 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'data-input-vignette.tex' (20652 bytes), 'differences.R' (53 bytes), 'differences.Rnw' (5962 bytes), 'differences.tex' (6059 bytes), 'imputation-vignette-best.pdf' (12365 bytes), 'imputation-vignette-compare.pdf' (15901 bytes), 'imputation-vignette-imptest-rhs.pdf' (15894 bytes), 'imputation-vignette-mach.pdf' (5362 bytes), 'imputation-vignette-rsqmaf.pdf' (36322 bytes), 'imputation-vignette-ruleplot.pdf' (4784 bytes), 'imputation-vignette-uncert1.pdf' (4685 bytes), 'imputation-vignette-uncert2.pdf' (4783 bytes), 'imputation-vignette.R' (6625 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'imputation-vignette.tex' (23171 bytes), 'index.html' (2023 bytes), 'ld-vignette-clplot.pdf' (6316 bytes), 'ld-vignette-dpplot1.pdf' (7340 bytes), 'ld-vignette-dpplot2.pdf' (6332 bytes), 'ld-vignette-drplot.pdf' (12831 bytes), 'ld-vignette-eplot.pdf' (16096 bytes), 'ld-vignette-image1a.pdf' (232994 bytes), 'ld-vignette-image2a.pdf' (239457 bytes), 'ld-vignette-image3a.pdf' (66745 bytes), 'ld-vignette-image4a.pdf' (60700 bytes), 'ld-vignette-imagecola.pdf' (224839 bytes), 'ld-vignette.R' (7240 bytes), 'ld-vignette.Rnw' (12641 bytes), 'ld-vignette.tex' (15175 bytes), 'pca-vignette-pc-one.pdf' (5944 bytes), 'pca-vignette-testing.pdf' (146512 bytes), 'pca-vignette.R' (1863 bytes), 'pca-vignette.Rnw' (9345 bytes), 'pca-vignette.tex' (10194 bytes), 'snpStats-vignette-more-tests-qq.pdf' (76448 bytes), 'snpStats-vignette-more-tests.pdf' (20618 bytes), 'snpStats-vignette-plot-freqs.pdf' (17737 bytes), 'snpStats-vignette-plot-mtests.pdf' (20854 bytes), 'snpStats-vignette-plot-outliners-qc.pdf' (209132 bytes), 'snpStats-vignette-plot-snpsum.pdf' (4806 bytes), 'snpStats-vignette-plot-summaries.pdf' (9625 bytes), 'snpStats-vignette-plot-tests.pdf' (22724 bytes), 'snpStats-vignette-qqplot-mtests.pdf' (46267 bytes), 'snpStats-vignette-qqplot.pdf' (76359 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'snpStats-vignette.tex' (33226 bytes), 'tdt-vignette.Rnw' (5171 bytes)
--- failed re-building 'snpStats-vignette.Rnw'

--- re-building 'tdt-vignette.Rnw' using Sweave
Warning in tdt.snp(data = pedData, snp.data = genotypes) :
  211 misinheritances were detected
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "tdt-vignette.tex" --max-iterations=20 -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/tex/latex" -I "C:/Users/bioctesting/bbs-3.11-bioc-testing/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'tdt-vignette.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'tdt-vignette.pdf' for vignette with name 'tdt-vignette' and engine 'utils::Sweave'. The following files exist in working directory 'C:\Users\bioctesting\bbs-3.11-bioc-testing\tmpdir\RtmpsjcBx6\Rbuildde0291c6c4e\snpStats\vignettes': 'Fst-vignette.R' (885 bytes), 'Fst-vignette.Rnw' (4429 bytes), 'Fst-vignette.tex' (4777 bytes), 'data-input-vignette.R' (3287 bytes), 'data-input-vignette.Rnw' (12239 bytes), 'data-input-vignette.tex' (20652 bytes), 'differences.R' (53 bytes), 'differences.Rnw' (5962 bytes), 'differences.tex' (6059 bytes), 'imputation-vignette-best.pdf' (12365 bytes), 'imputation-vignette-compare.pdf' (15901 bytes), 'imputation-vignette-imptest-rhs.pdf' (15894 bytes), 'imputation-vignette-mach.pdf' (5362 bytes), 'imputation-vignette-rsqmaf.pdf' (36322 bytes), 'imputation-vignette-ruleplot.pdf' (4784 bytes), 'imputation-vignette-uncert1.pdf' (4685 bytes), 'imputation-vignette-uncert2.pdf' (4783 bytes), 'imputation-vignette.R' (6625 bytes), 'imputation-vignette.Rnw' (15762 bytes), 'imputation-vignette.tex' (23171 bytes), 'index.html' (2023 bytes), 'ld-vignette-clplot.pdf' (6316 bytes), 'ld-vignette-dpplot1.pdf' (7340 bytes), 'ld-vignette-dpplot2.pdf' (6332 bytes), 'ld-vignette-drplot.pdf' (12831 bytes), 'ld-vignette-eplot.pdf' (16096 bytes), 'ld-vignette-image1a.pdf' (232994 bytes), 'ld-vignette-image2a.pdf' (239457 bytes), 'ld-vignette-image3a.pdf' (66745 bytes), 'ld-vignette-image4a.pdf' (60700 bytes), 'ld-vignette-imagecola.pdf' (224839 bytes), 'ld-vignette.R' (7240 bytes), 'ld-vignette.Rnw' (12641 bytes), 'ld-vignette.tex' (15175 bytes), 'pca-vignette-pc-one.pdf' (5944 bytes), 'pca-vignette-testing.pdf' (146512 bytes), 'pca-vignette.R' (1863 bytes), 'pca-vignette.Rnw' (9345 bytes), 'pca-vignette.tex' (10194 bytes), 'snpStats-vignette-more-tests-qq.pdf' (76448 bytes), 'snpStats-vignette-more-tests.pdf' (20618 bytes), 'snpStats-vignette-plot-freqs.pdf' (17737 bytes), 'snpStats-vignette-plot-mtests.pdf' (20854 bytes), 'snpStats-vignette-plot-outliners-qc.pdf' (209132 bytes), 'snpStats-vignette-plot-snpsum.pdf' (4806 bytes), 'snpStats-vignette-plot-summaries.pdf' (9625 bytes), 'snpStats-vignette-plot-tests.pdf' (22724 bytes), 'snpStats-vignette-qqplot-mtests.pdf' (46267 bytes), 'snpStats-vignette-qqplot.pdf' (76359 bytes), 'snpStats-vignette.R' (8542 bytes), 'snpStats-vignette.Rnw' (21155 bytes), 'snpStats-vignette.tex' (33226 bytes), 'tdt-vignette-per-family.pdf' (4494 bytes), 'tdt-vignette-per-subj-snp.pdf' (4705 bytes), 'tdt-vignette-tdt-tests.pdf' (7526 bytes), 'tdt-vignette.Rnw' (5171 bytes), 'tdt-vignette.tex' (8001 bytes)
--- failed re-building 'tdt-vignette.Rnw'

SUMMARY: processing the following files failed:
  'Fst-vignette.Rnw' 'data-input-vignette.Rnw' 'differences.Rnw'
  'imputation-vignette.Rnw' 'ld-vignette.Rnw' 'pca-vignette.Rnw'
  'snpStats-vignette.Rnw' 'tdt-vignette.Rnw'

Error: Vignette re-building failed.
Execution halted