Displaying 7 results from an estimated 7 matches for "biocstyl".
Did you mean:
biocstyle
2014 Jun 14
1
Should a package that indirectly Suggests: a vignette engine pass R CMD check?
A package uses VignetteEngine: knitr; the package itself does not Suggests:
knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R
CMD check fails indicating that a package required for checking is not declared.
Is it really the intention that the original package duplicate Suggests: knitr?
This is only with a recent R. In detail, with
$ Rdev --version|head -3
R Under developm...
2018 Sep 18
2
Suggested Patch: Adding commas to list of packages after R CMD check
...;dplyr' 'readr' 'ggplot2' 'ggfortify' 'reshape2' 'rlang' 'loose.rock'
Packages suggested but not available:
'testthat' 'knitr' 'rmarkdown' 'survcomp' 'pROC' 'devtools'
'VennDiagram' 'BiocStyle' 'curatedTCGAData'
VignetteBuilder package required for checking but not installed: 'knitr'
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See sec...
2018 Feb 07
1
release build of ChemmineR failing
...ing on windows. It seems to be a
build script issue though, possibly something on your side. The package
was building fine a few weeks ago and I have not modified it. Can you
please have a look? Thanks.
"C:/Users/BIOCBU?1/BBS-3?1.6-B/R/bin/Rscript" -e "library(rmarkdown); library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
'C:\Users\BIOCBU?1\BBS-3?1.6-B\R\bin\x64\Rscript.exe" -e "library' is not recognized as an internal or external command,operable program or batch file.
http://bioconductor.org/checkResults/release/bioc-LATEST/ChemmineR/tokay1-bu...
2014 Nov 13
3
Changing style for the Sweave vignettes
As a user, I am always annoyed beyond measure that Sweave vignettes
precede the code by a command line prompt. It makes running examples
by simple copying of the commands from the vignette to the console a
pain. I know the idea is that it is clear what is the command, and
what is the output, but I'd rather precede the output with some kind
of marking.
Is there any other solution possible /
2018 Sep 18
0
Suggested Patch: Adding commas to list of packages after R CMD check
...' 'ggplot2' 'ggfortify' 'reshape2' 'rlang' 'loose.rock'
>
> Packages suggested but not available:
> 'testthat' 'knitr' 'rmarkdown' 'survcomp' 'pROC' 'devtools'
> 'VennDiagram' 'BiocStyle' 'curatedTCGAData'
>
> VignetteBuilder package required for checking but not installed: 'knitr'
>
> The suggested packages are required for a complete check.
> Checking can be attempted without them by setting the environment
> variable _R_CHECK_FORCE_SUGGES...
2015 May 14
1
Creating a vignette which depends on a non-distributable file
...ave unit tests or other approaches to ensure that 'bit rot' does
not set in without you being aware of it.
If this is a Bioconductor package, then it's appropriate to ask on the
Bioconductor devel mailing list.
http://bioconductor.org/developers/
http://bioconductor.org/packages/BiocStyle/ might be your friend for producing
stylish vignettes.
Martin
>> (3) I could build vignette outside of the package and put it into the
>> inst/doc directory. This also has obvious drawbacks.
>> (4) Leaving this example out defies the purpose of my package.
>>
>> I...
2015 May 14
2
Creating a vignette which depends on a non-distributable file
Dear all,
I am writing a vignette that requires a file which I am not allowed to
distribute, but which the user can easily download manually. Moreover, it
is not possible to download this file automatically from R: downloading
requires a (free) registration that seems to work only through a browser.
(I'm talking here about the MSigDB from the Broad Institute,