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###
### Running command:
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###   chmod a+r genphen -R && C:\Users\biocbuild\bbs-3.12-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-3~1.12-/R/etc/x64/Makeconf" -f "C:/Users/BIOCBU~1/BBS-3~1.12-/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file2b1c355e953.dll" WIN=64 TCLBIN=64 OBJECTS="file2b1c355e953.o"

make would use
if test "zfile2b1c355e953.o" != "z"; then \
  if test -e "file2b1c355e953-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file2b1c355e953.dll file2b1c355e953-win.def file2b1c355e953.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file2b1c355e953.dll file2b1c355e953-win.def file2b1c355e953.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file2b1c355e953.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 file2b1c355e953.dll tmp.def file2b1c355e953.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file2b1c355e953.dll tmp.def file2b1c355e953.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"C:/Users/BIOCBU~1/BBS-3~1.12-/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