Error: processing vignette 'ISBCancerGenomicsCloud.Rmd' failed with diagnostics:

[tedgoldstein]

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install_github("isb-cgc/examples-R", build_vignettes=TRUE)
Downloading GitHub repo isb-cgc/examples-R@master
from URL https://api.github.com/repos/isb-cgc/examples-R/zipball/master
Installing ISBCGCExamples
trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/bigrquery_0.3.0.tgz'

Content type 'application/x-gzip' length 147255 bytes (143 KB)

downloaded 143 KB

Installing bigrquery
trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/assertthat_0.1.tgz'

Content type 'application/x-gzip' length 43319 bytes (42 KB)

downloaded 42 KB

Installing assertthat
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9584d30d5bf/assertthat'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
--install-tests

• installing binary package ‘assertthat’ ...

• DONE (assertthat)
  trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/DBI_0.5-1.tgz'
  Content type 'application/x-gzip' length 353725 bytes (345 KB)

  downloaded 345 KB

Installing DBI
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools95863dde744/DBI'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
--install-tests

• installing binary package ‘DBI’ ...

• DONE (DBI)
  trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/dplyr_0.5.0.tgz'
  Content type 'application/x-gzip' length 4843092 bytes (4.6 MB)

  downloaded 4.6 MB

Installing dplyr
trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/BH_1.60.0-2.tgz'

Content type 'application/x-gzip' length 9263128 bytes (8.8 MB)

downloaded 8.8 MB

Installing BH
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9586dc278cf/BH'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
--install-tests

• installing binary package ‘BH’ ...

• DONE (BH)
  trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/lazyeval_0.2.0.tgz'
  Content type 'application/x-gzip' length 122448 bytes (119 KB)

  downloaded 119 KB

Installing lazyeval
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9581ebd653/lazyeval'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
--install-tests

• installing binary package ‘lazyeval’ ...

• DONE (lazyeval)
  trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/Rcpp_0.12.7.tgz'
  Content type 'application/x-gzip' length 2989753 bytes (2.9 MB)

  downloaded 2.9 MB

Installing Rcpp
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9586bb112dd/Rcpp'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
--install-tests

• installing binary package ‘Rcpp’ ...

• DONE (Rcpp)
  trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/tibble_1.2.tgz'
  Content type 'application/x-gzip' length 294143 bytes (287 KB)

  downloaded 287 KB

Installing tibble
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9586f1fd010/tibble'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
--install-tests

• installing binary package ‘tibble’ ...
• DONE (tibble)
  '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
  --no-save --no-restore --quiet CMD INSTALL
  '/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9585b8c7433/dplyr'
  --library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
  --install-tests
• installing binary package ‘dplyr’ ...

• DONE (dplyr)
  trying URL 'https://cran.cnr.berkeley.edu/bin/macosx/mavericks/contrib/3.2/jsonlite_1.1.tgz'
  Content type 'application/x-gzip' length 1104984 bytes (1.1 MB)

  downloaded 1.1 MB

Installing jsonlite
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools95821296f27/jsonlite'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
--install-tests

• installing binary package ‘jsonlite’ ...
• DONE (jsonlite)
  '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
  --no-save --no-restore --quiet CMD INSTALL
  '/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools958636b0c54/bigrquery'
  --library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library'
  --install-tests
• installing binary package ‘bigrquery’ ...
• DONE (bigrquery)
  '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
  --no-save --no-restore --quiet CMD build
  '/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9583e900d92/isb-cgc-examples-R-4f42f54'
  --no-resave-data --no-manual
• checking for file ‘/private/var/folders/gz/fc2cq05d0wd25tvnb3mslg240000gn/T/Rtmplvp6tY/devtools9583e900d92/isb-cgc-examples-R-4f42f54/DESCRIPTION’ ... OK
• preparing ‘ISBCGCExamples’:
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ... ERROR
  Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
  Error: processing vignette 'ISBCancerGenomicsCloud.Rmd' failed with diagnostics:
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because ISBCancerGenomicsCloud.Rmd appears to be an R Markdown v2 document.
  Execution halted

[Gibbsdavidl]

Hi there @tedgoldstein,

Thanks for letting me know! Could you "do a git pull" and try again? I've changed the vignette builder to rmarkdown... seems to work on my machine, but let me know if that doesn't work for you.

Thanks!
-dave