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BUILD report for genphen on tokay2

This page was generated on 2020-10-17 11:56:40 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE genphen PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 718/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genphen 1.16.0
Simo Kitanovski
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/genphen
Branch: RELEASE_3_11
Last Commit: a348d23
Last Changed Date: 2020-04-27 14:56:02 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK [ ERROR ] skipped  skipped 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genphen
Version: 1.16.0
Command: chmod a+r genphen -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data genphen
StartedAt: 2020-10-16 21:56:15 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 21:57:48 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 93.1 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r genphen -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data genphen
###
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* checking for file 'genphen/DESCRIPTION' ... OK
* preparing 'genphen':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'genphenManual.Rnw' using Sweave
Loading required package: genphen
Loading required package: Rcpp
Loading required package: ggplot2
Loading required package: knitr
Loading required package: ggrepel
Loading required package: reshape
Loading required package: ape
Loading required package: xtable
Loading required package: gridExtra
make cmd is
  make -f "C:/Users/BIOCBU~1/BBS-3~1.11-/R/etc/x64/Makeconf" -f "C:/Users/BIOCBU~1/BBS-3~1.11-/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file12886e6751bf.dll" WIN=64 TCLBIN=64 OBJECTS="file12886e6751bf.o"

make would use
if test "zfile12886e6751bf.o" != "z"; then \
  if test -e "file12886e6751bf-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file12886e6751bf.dll file12886e6751bf-win.def file12886e6751bf.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file12886e6751bf.dll file12886e6751bf-win.def file12886e6751bf.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file12886e6751bf.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g'  >> tmp.def; \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file12886e6751bf.dll tmp.def file12886e6751bf.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file12886e6751bf.dll tmp.def file12886e6751bf.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi

Error: processing vignette 'genphenManual.Rnw' failed with diagnostics:
 chunk 6 
Error in sink(type = "output") : invalid connection

--- failed re-building 'genphenManual.Rnw'

SUMMARY: processing the following file failed:
  'genphenManual.Rnw'

Error: Vignette re-building failed.
Execution halted