Error in re-building vignettes:
  ...
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 'https://cloud.r-project.org/src/contrib/assertthat_0.2.0.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz'
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* installing *source* package ‘assertthat’ ...
** package ‘assertthat’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (assertthat)
* installing *source* package ‘crayon’ ...
** package ‘crayon’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (crayon)
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c aes.c -o aes.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c crc32.c -o crc32.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c digest.c -o digest.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c init.c -o init.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c md5.c -o md5.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c pmurhash.c -o pmurhash.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c raes.c -o raes.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c sha1.c -o sha1.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c sha2.c -o sha2.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c sha256.c -o sha256.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c xxhash.c -o xxhash.o
cc -xc99 -G -L/usr/local/lib -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o
installing to /tmp/RtmpeJaimM/folder1/digest/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
* DONE (digest)
* installing *source* package ‘magrittr’ ...
** package ‘magrittr’ successfully unpacked and MD5 sums checked
** 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
* DONE (magrittr)
* installing *source* package ‘praise’ ...
** package ‘praise’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (praise)
* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** 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
* DONE (R6)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** libs
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I./lib/  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c capture.c -o capture.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I./lib/  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c export.c -o export.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I./lib/  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c internal.c -o internal.o
"internal/expr-interp.c", line 64: warning: statement not reached
"internal/expr-interp.c", line 71: warning: statement not reached
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I./lib/  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c lib.c -o lib.o
"lib/squash.c", line 211: warning: statement not reached
"lib/squash.c", line 262: warning: statement not reached
cc -xc99 -G -L/usr/local/lib -o rlang.so capture.o export.o internal.o lib.o
installing to /tmp/RtmpeJaimM/folder1/rlang/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
* DONE (rlang)
* installing *source* package ‘withr’ ...
** package ‘withr’ successfully unpacked and MD5 sums checked
** 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
* DONE (withr)
* installing *source* package ‘pls’ ...
** package ‘pls’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (pls)
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** 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
* DONE (cli)
* installing *source* package ‘apercu’ ...
** package ‘apercu’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (apercu)
* installing *source* package ‘testthat’ ...
** package ‘testthat’ successfully unpacked and MD5 sums checked
** libs
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c init.c -o init.o
cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/usr/local/include   -KPIC  -O -xlibmieee -xlibmil -xtarget=native -nofstore  -c reassign.c -o reassign.o
CC -library=stlport4 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/usr/local/include   -KPIC  -O -xlibmil -xtarget=native -nofstore  -c test-catch.cpp -o test-catch.o
CC -library=stlport4 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/usr/local/include   -KPIC  -O -xlibmil -xtarget=native -nofstore  -c test-example.cpp -o test-example.o
CC -library=stlport4 -I"/home/ripley/R/cc/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/usr/local/include   -KPIC  -O -xlibmil -xtarget=native -nofstore  -c test-runner.cpp -o test-runner.o
CC -library=stlport4 -G -L/usr/local/lib -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o
installing to /tmp/RtmpeJaimM/folder1/testthat/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
* DONE (testthat)

The downloaded source packages are in
	'/tmp/RtmpeJaimM/downloaded_packages'
* installing *source* package ‘dummyPackage’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (dummyPackage)
Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/src/contrib/apercu_0.2.3.tar.gz'
Content type 'application/x-gzip' length 7010 bytes
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downloaded 7010 bytes

* installing *source* package ‘apercu’ ...
** package ‘apercu’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (apercu)

The downloaded source packages are in
	'/tmp/RtmpeJaimM/downloaded_packages'
Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/src/contrib/apercu_0.2.3.tar.gz'
Content type 'application/x-gzip' length 7010 bytes
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downloaded 7010 bytes

* installing *source* package ‘apercu’ ...
** package ‘apercu’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (apercu)

The downloaded source packages are in
	'/tmp/RtmpeJaimM/downloaded_packages'
Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/src/contrib/apercu_0.2.3.tar.gz'
Content type 'application/x-gzip' length 7010 bytes
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downloaded 7010 bytes

* installing *source* package ‘apercu’ ...
** package ‘apercu’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (apercu)

The downloaded source packages are in
	'/tmp/RtmpeJaimM/downloaded_packages'
Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
Error: processing vignette 'help.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted