Error(s) in re-building vignettes:
  ...
--- re-building ‘muHVT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'http://cran.us.r-project.org/src/contrib/ps_1.3.1.tar.gz'
Content type 'application/octet-stream' length 98722 bytes (96 KB)
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downloaded 96 KB

trying URL 'http://cran.us.r-project.org/src/contrib/processx_3.4.2.tar.gz'
Content type 'application/octet-stream' length 130148 bytes (127 KB)
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trying URL 'http://cran.us.r-project.org/src/contrib/selectr_0.4-2.tar.gz'
Content type 'application/octet-stream' length 41371 bytes (40 KB)
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trying URL 'http://cran.us.r-project.org/src/contrib/hms_0.5.3.tar.gz'
Content type 'application/octet-stream' length 134669 bytes (131 KB)
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trying URL 'http://cran.us.r-project.org/src/contrib/clipr_0.7.0.tar.gz'
Content type 'application/octet-stream' length 20381 bytes (19 KB)
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trying URL 'http://cran.us.r-project.org/src/contrib/callr_3.4.2.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/xml2_1.2.2.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/rvest_0.3.5.tar.gz'
Content type 'application/octet-stream' length 1129355 bytes (1.1 MB)
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trying URL 'http://cran.us.r-project.org/src/contrib/readr_1.3.1.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/webshot_0.5.2.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/R.oo_1.23.0.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/R.methodsS3_1.7.1.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/kableExtra_1.1.0.tar.gz'
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downloaded 1.4 MB

trying URL 'http://cran.us.r-project.org/src/contrib/R.utils_2.9.2.tar.gz'
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* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/cc -xc99 -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -Wall px.c -o px
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c init.c -o init.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c api-common.c -o api-common.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c common.c -o common.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c extra.c -o extra.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c dummy.c -o dummy.o
"dummy.c", line 68: syntax error before or at: x
"dummy.c", line 68: warning: undefined or missing type for: x
"dummy.c", line 82: syntax error before or at: x
"dummy.c", line 82: warning: undefined or missing type for: x
cc: acomp failed for dummy.c
*** Error code 2
make: Fatal error: Command failed for target `dummy.o'
Current working directory /tmp/RtmpmTaa7S/R.INSTALL59d84c355c4c/ps/src
ERROR: compilation failed for package ‘ps’
* removing ‘/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/ps’
Warning in install.packages(new.packages, repos = "http://cran.us.r-project.org") :
  installation of package 'ps' had non-zero exit status
* installing *source* package ‘selectr’ ...
** package ‘selectr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (selectr)
* installing *source* package ‘hms’ ...
** package ‘hms’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hms)
* installing *source* package ‘clipr’ ...
** package ‘clipr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clipr)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/local/include/libxml2 -I/usr/local/include
Using PKG_LIBS=-L/usr/local/lib -R/usr/local/lib -lxml2 -L/opt/csw/lib -lz -lpthread -L/usr/local/lib -liconv -lm -lsocket -lnsl
** libs
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c RcppExports.cpp -o RcppExports.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c connection.cpp -o connection.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_doc.cpp -o xml2_doc.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_init.cpp -o xml2_init.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_namespace.cpp -o xml2_namespace.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_node.cpp -o xml2_node.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_output.cpp -o xml2_output.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_schema.cpp -o xml2_schema.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_url.cpp -o xml2_url.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -I/usr/local/include/libxml2 -I/usr/local/include -DUCHAR_TYPE=wchar_t -I"/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/Rcpp/include" -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xml2_xpath.cpp -o xml2_xpath.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -G -L/usr/local/lib -o xml2.so RcppExports.o connection.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -L/usr/local/lib -R/usr/local/lib -lxml2 -L/opt/csw/lib -lz -lpthread -L/usr/local/lib -liconv -lm -lsocket -lnsl
installing to /tmp/RtmpLCaaTY/RLIBS_65683a3669ef/00LOCK-xml2/00new/xml2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xml2)
* installing *source* package ‘R.methodsS3’ ...
** package ‘R.methodsS3’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R.methodsS3)
ERROR: dependency ‘ps’ is not available for package ‘processx’
* removing ‘/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/processx’
Warning in install.packages(new.packages, repos = "http://cran.us.r-project.org") :
  installation of package 'processx' had non-zero exit status
* installing *source* package ‘rvest’ ...
** package ‘rvest’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rvest)
* installing *source* package ‘readr’ ...
** package ‘readr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make: Fatal error in reader: Makevars, line 4: Unexpected end of line seen
Current working directory /tmp/RtmpQBaa13/R.INSTALL6fa84842610a/readr/src
ERROR: compilation failed for package ‘readr’
* removing ‘/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/readr’
Warning in install.packages(new.packages, repos = "http://cran.us.r-project.org") :
  installation of package 'readr' had non-zero exit status
* installing *source* package ‘R.oo’ ...
** package ‘R.oo’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R.oo)
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/callr’
Warning in install.packages(new.packages, repos = "http://cran.us.r-project.org") :
  installation of package 'callr' had non-zero exit status
* installing *source* package ‘R.utils’ ...
** package ‘R.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function warnings to warnings.default, which was defined in environment base.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R.utils)
ERROR: dependency ‘callr’ is not available for package ‘webshot’
* removing ‘/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/webshot’
Warning in install.packages(new.packages, repos = "http://cran.us.r-project.org") :
  installation of package 'webshot' had non-zero exit status
ERROR: dependencies ‘readr’, ‘webshot’ are not available for package ‘kableExtra’
* removing ‘/tmp/RtmpLCaaTY/RLIBS_65683a3669ef/kableExtra’
Warning in install.packages(new.packages, repos = "http://cran.us.r-project.org") :
  installation of package 'kableExtra' had non-zero exit status

The downloaded source packages are in
	'/tmp/RtmpiRaOjk/downloaded_packages'
Quitting from lines 18-121 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building ‘muHVT.Rmd’

SUMMARY: processing the following file failed:
  ‘muHVT.Rmd’

Error: Vignette re-building failed.
Execution halted