I need some help understanding a problem running the tests on the
'digest' package. Initially, I got the message that the 'knitr' package
was needed to run vignettes:
Running vignettes for package ?digest?
Error in loadVignetteBuilder(vigns$pkgdir) :
vignette builder 'knitr' not found
So I installed the knitr package and all its dependents (?mime?,
?stringi?, ?magrittr?, ?evaluate?, ?formatR?, ?highr?, ?markdown?,
?stringr?, ?yaml?) . Now I get some different warnings:
Running vignettes for package ?digest?
Running ?sha1.Rmd?
Warning messages:
1: In readLines(if (is.character(input2)) { :
cannot open file 'sha1.Rmd': No such file or directory
2: In engine$weave(file, quiet = TRUE, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the
rmarkdown package is not installed. Please install it.
3: In readLines(con) :
cannot open file 'sha1.Rmd': No such file or directory
So why is sha1.Rmd missing? And why is it complaining about rmarkdown?
Or more precisely why did it not install it as a dependent? It installed
plain markdown.
Mick Jordan
vignette/knitr help
5 messages · Mick Jordan, Thierry Onkelinx
Dear Mick, Note that both knitr and rmarkdown are listed under Suggests: both are required to compile the vignette. Installing rmarkdown should solve the problem. If not, please provide more information. OS, R version, digest version, ... Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2016-05-03 20:10 GMT+02:00 Mick Jordan <mick.jordan at oracle.com>:
I need some help understanding a problem running the tests on the 'digest'
package. Initially, I got the message that the 'knitr' package was needed to
run vignettes:
Running vignettes for package ?digest?
Error in loadVignetteBuilder(vigns$pkgdir) :
vignette builder 'knitr' not found
So I installed the knitr package and all its dependents (?mime?, ?stringi?,
?magrittr?, ?evaluate?, ?formatR?, ?highr?, ?markdown?, ?stringr?, ?yaml?) .
Now I get some different warnings:
Running vignettes for package ?digest?
Running ?sha1.Rmd?
Warning messages:
1: In readLines(if (is.character(input2)) { :
cannot open file 'sha1.Rmd': No such file or directory
2: In engine$weave(file, quiet = TRUE, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the
rmarkdown package is not installed. Please install it.
3: In readLines(con) :
cannot open file 'sha1.Rmd': No such file or directory
So why is sha1.Rmd missing? And why is it complaining about rmarkdown? Or
more precisely why did it not install it as a dependent? It installed plain
markdown.
Mick Jordan
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
On 5/3/16 11:29 AM, Thierry Onkelinx wrote:
Dear Mick, Note that both knitr and rmarkdown are listed under Suggests: both are required to compile the vignette. Installing rmarkdown should solve the problem. If not, please provide more information. OS, R version, digest version, ...
This is occurring in the context of an automated testing environment that compares the output of GnuR and FastR. I'm using tools::testInstalledPackage with the default values for 'types'. I guess the problem is that there is no connection between this step and the previous package install step (that did use --install-tests) but didn't install the "Suggests" dependencies because in general these are not needed. But I still am not clear why knitr doesn't list rmarkdown as a dependency when it clearly will try to use it. To me that is is not "Suggests" dependency. Mick
Dear Mick, knitr doesn't depends on rmarkdown. It's the vignette that depends on both knitr (for handle the R chunks) and rmarkdown (for the output format rmarkdown::html_vignette). https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies states: "The ?Suggests? field ...snip... lists packages that are not necessarily needed. This includes packages used only in examples, tests or vignettes ...snip... Then it is not necessary to have bar use foo unless one wants to execute all the examples/tests/vignettes" So packages in Suggests might be required to compile vignettes. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2016-05-03 21:05 GMT+02:00 Mick Jordan <mick.jordan at oracle.com>:
On 5/3/16 11:29 AM, Thierry Onkelinx wrote:
Dear Mick, Note that both knitr and rmarkdown are listed under Suggests: both are required to compile the vignette. Installing rmarkdown should solve the problem. If not, please provide more information. OS, R version, digest version, ...
This is occurring in the context of an automated testing environment that compares the output of GnuR and FastR. I'm using tools::testInstalledPackage with the default values for 'types'. I guess the problem is that there is no connection between this step and the previous package install step (that did use --install-tests) but didn't install the "Suggests" dependencies because in general these are not needed. But I still am not clear why knitr doesn't list rmarkdown as a dependency when it clearly will try to use it. To me that is is not "Suggests" dependency. Mick
On 5/3/16 12:19 PM, Thierry Onkelinx wrote:
Dear Mick, knitr doesn't depends on rmarkdown. It's the vignette that depends on both knitr (for handle the R chunks) and rmarkdown (for the output format rmarkdown::html_vignette). https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies states: "The ?Suggests? field ...snip... lists packages that are not necessarily needed. This includes packages used only in examples, tests or vignettes ...snip... Then it is not necessary to have bar use foo unless one wants to execute all the examples/tests/vignettes" So packages in Suggests might be required to compile vignettes.
Ok, I get it now, and a more careful reading of the Writing Extensions
manual would have helped prevent the surprise. Anyway, FastR can't
handle knitr yet so I am backing off to testing types=c("examples, "tests").
Thanks
Mick