Error(s) in re-building vignettes:
  ...
--- re-building ‘batch-mode.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.
--- finished re-building ‘batch-mode.Rmd’

--- re-building ‘linescan-data.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.
--- finished re-building ‘linescan-data.Rmd’

--- re-building ‘single-images.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.rstudio.com/src/contrib/colorspace_1.4-1.tar.gz'
Content type 'application/x-gzip' length 2152594 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'http://cran.rstudio.com/src/contrib/farver_2.0.3.tar.gz'
Content type 'application/x-gzip' length 1279579 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'http://cran.rstudio.com/src/contrib/labeling_0.3.tar.gz'
Content type 'application/x-gzip' length 10722 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'http://cran.rstudio.com/src/contrib/munsell_0.5.0.tar.gz'
Content type 'application/x-gzip' length 182653 bytes (178 KB)
==================================================
downloaded 178 KB

trying URL 'http://cran.rstudio.com/src/contrib/RColorBrewer_1.1-2.tar.gz'
Content type 'application/x-gzip' length 11532 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'http://cran.rstudio.com/src/contrib/viridisLite_0.3.0.tar.gz'
Content type 'application/x-gzip' length 44019 bytes (42 KB)
==================================================
downloaded 42 KB

trying URL 'http://cran.rstudio.com/src/contrib/isoband_0.2.0.tar.gz'
Content type 'application/x-gzip' length 1894070 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'http://cran.rstudio.com/src/contrib/scales_1.1.0.tar.gz'
Content type 'application/x-gzip' length 510666 bytes (498 KB)
==================================================
downloaded 498 KB

trying URL 'http://cran.rstudio.com/src/contrib/ggplot2_3.3.0.tar.gz'
Content type 'application/x-gzip' length 3031461 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc-devel/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c colorspace.c -o colorspace.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc-devel/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 -G -L/usr/local/lib -o colorspace.so colorspace.o init.o
installing to /tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/00LOCK-colorspace/00new/colorspace/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** 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 (colorspace)
* installing *source* package ‘farver’ ...
** package ‘farver’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c ColorSpace.cpp -o ColorSpace.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c Comparison.cpp -o Comparison.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c Conversion.cpp -o Conversion.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c encode.cpp -o encode.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c farver.cpp -o farver.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c init.cpp -o init.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -G -L/usr/local/lib -o farver.so ColorSpace.o Comparison.o Conversion.o encode.o farver.o init.o
installing to /tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/00LOCK-farver/00new/farver/libs
** 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
Error: package or namespace load failed for ‘farver’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/00LOCK-farver/00new/farver/libs/farver.so':
  ld.so.1: R: fatal: relocation error: file /tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/00LOCK-farver/00new/farver/libs/farver.so: symbol __cxa_pure_virtual: referenced symbol not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/farver’
* installing *source* package ‘labeling’ ...
** package ‘labeling’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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 (labeling)
* installing *source* package ‘RColorBrewer’ ...
** package ‘RColorBrewer’ 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 (RColorBrewer)
* installing *source* package ‘viridisLite’ ...
** package ‘viridisLite’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (viridisLite)
* installing *source* package ‘isoband’ ...
** package ‘isoband’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/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 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c clip-lines.cpp -o clip-lines.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c isoband.cpp -o isoband.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c polygon.cpp -o polygon.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c separate-polygons.cpp -o separate-polygons.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c test-clip-lines.cpp -o test-clip-lines.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c test-runner.cpp -o test-runner.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -I"/home/ripley/R/cc-devel/include" -DNDEBUG  -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/Rcpp/include' -I'/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/testthat/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c test-separate-polygons.cpp -o test-separate-polygons.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -G -L/usr/local/lib -o isoband.so RcppExports.o clip-lines.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o
installing to /tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/00LOCK-isoband/00new/isoband/libs
** R
** 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
Error: package or namespace load failed for ‘isoband’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/00LOCK-isoband/00new/isoband/libs/isoband.so':
  ld.so.1: R: fatal: relocation error: file /tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/00LOCK-isoband/00new/isoband/libs/isoband.so: symbol _ZNSoD1Ev: referenced symbol not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/isoband’
* installing *source* package ‘munsell’ ...
** package ‘munsell’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** 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 (munsell)
ERROR: dependency ‘farver’ is not available for package ‘scales’
* removing ‘/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/scales’
ERROR: dependencies ‘isoband’, ‘scales’ are not available for package ‘ggplot2’
* removing ‘/tmp/Rtmp5NaycM/RLIBS_4c1318a36ef/ggplot2’

The downloaded source packages are in
	'/tmp/Rtmp5NaycM/working_dir/RtmpYwaiLp/downloaded_packages'
Quitting from lines 48-66 (single-images.Rmd) 
Error: processing vignette 'single-images.Rmd' failed with diagnostics:
could not find function "ggplot"
--- failed re-building ‘single-images.Rmd’

SUMMARY: processing the following file failed:
  ‘single-images.Rmd’

Error: Vignette re-building failed.
Execution halted