I just recently submitted an update of my package to CRAN, and I was notified that a line in an .Rd file was too wide. Using the latest Rpatched version, I ran the R CMD check, everything checked out ok. I ran the --as-cran on the tarball and everything is ok. When I examined the .PDF file created after R CMD build, I do see that the line in the .PDF help file extended beyond page margin.
My question is where and how do I check for errors in the creation of the .PDF file? I've checked through Writing R Extensions, etc. and I can't find a specific statement.
Build and check your package R CMD build mypkg && R CMD check mypkg_1.2.3.tar.gz. Then look in mypkg.Rcheck/Rdlatex.log for warnings (like Overful \hbox) while processing the Rd file to latex.
Related
For reasons that are too long to explain here, I must use R.2.8.1 (unfortunately). I need to have the xlsx package installed on it. Since I am on R 2.8.1, about ten years old, I can't use the latest version of xlsx but an older version, for instance xlsx_0.1.3 from 2010 seems a good choice. However the previous releases per R-CRAN policy are only available in tar.gz.
This is very unfortunate to me because I have to use RGui on windows which only accepts .Zip packages in installation. Therefore I tried the following stuff, in vain:
1-I tried to use Rcmd but I get the following error message:
C:\Program Files (x86)\R\R-2.8.1\bin>Rcmd INSTALL C:\Users\username\Downloads\xlsx_0.1.3.tar.gz
Can't use 'defined(#array)' (Maybe you should just omit the defined()?) at C:\PROGRA~2\R\R-28~1.1/bin/INSTALL line 42.
so I give up on this one.
2-Then I think that the best solution is to convert the package xlsx_0.1.3.tar.gz into a compatible xlsx_0.1.3.zip package by building it using R.2.8.1 but I can't make it. Here is one of the things I have tried so far.
I have unziped xlsx_0.1.3.tar.gz and I organized it in the following way, which brought me the furthest:
Documents\xlsx
Documents\xlsx\activate.bat
Documents\xlsx\build_xlsx.bat
Documents\xlsx\R
Documents\xlsx\R\inst
Documents\xlsx\R\man
Documents\xlsx\R\other
Documents\xlsx\R\R
Documents\xlsx\R\DESCRIPTION
Documents\xlsx\R\NAMESPACE
Documents\xlsx\R\NEWS
Documents\xlsx\R\WISHLIST
inside activate.bat, I wrote:
SET TMP=C:\Users\username\Documents\TOTO\xlsx\tmp
SET TEMP=%TMP%
SET RTOOLSPATH=C:\DEV_307\toto\Rtools
SET RPATH=C:\DEV\toto\R\R-2.8.1
SET PATH=%RTOOLSPATH%\bin;%RTOOLSPATH%\MinGW\bin;%RPATH%\bin;%PATH%
inside build_xlsx.bat, I wrote:
R CMD BUILD R
R CMD check --no-examples --no-tests R
R CMD build --docs=normal --binary R
Then I still get:
C:\Users\username\Documents\TOTO\xlsx>R CMD BUILD R
* checking for file 'R/DESCRIPTION' ... OK
* preparing 'R':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
Can't use 'defined(#array)' (Maybe you should just omit the defined()?) at C:\DEV\toto\R\R-2.8.1/bin/INSTALL line 42.
ERROR
Installation failed.
Removing 'C:/Users/username/Documents/Rinst1210839349'
Thank you for your help
I can't include structured content in comments. This is really a comment.
The structure of source packages (which is what you have with xlsx_0.1.3.tar.gz if you pulled it from the CRAN archives) hasn't changed (much) since 2.8.1.
You'll also need to grab rJava_0.8-3.tar.gz and xlsxjars_0.2.0.tar.gz from the archive as xlsxjars + xlsx rely on rJava.
Extract each (since Windows R 2.8.1 seems to not grok gz files). They should make rJava, xlsxjars and xlsx directories each.
Move to the parent directory of both.
Run:
R CMD javareconf
R CMD build rJava
R CMD INSTALL rJava_0.8-3.zip # I believe this will be the name
R CMD build xlsxjars
R CMD INSTALL xlsxjars_0.2.0.zip
R CMD build xlsx
R CMD INSTALL xlsx_0.1.3.zip
and you should be gtg.
I'm preparing a package for submission to CRAN.
I use R CMD build myPackage then R CMD check myPackage --as-cran and it passes all checks with no notes or warnings.
However, each time I try to submit, I get the following error message from one of the CRAN maintainers:
Package has a VignetteBuilder field but no prebuilt vignette index.
As a start, I'd like to be able to reproduce the above error message on my own system (R version 3.0.1).
The vignette .Rnw file looks like this:
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{myVignetteName}
\documentclass{article}
\begin{document}
Here is some code:
<<>>=
plot(1:10, 10:100)
#
\end{document}
I have tried adding an INDEX file in the root directory with a vignette entry like this:
myFunction a brief description
abc-vignette vignette description
Again, this passes R CMD check myPackage --as-cran but I get the same error message.
I have also tried R CMD build myPackage --md5 to force creation of an MD5 file, to no avail.
When I look at myPackage.Rcheck/00_pkg_src/myPackage/inst/doc I find the vignette files, .Rnw and .pdf as expected.
The package DESCRIPTION file has the following entry:
VignetteBuilder: knitr
Suggests: knitr
When I look at myPackage.Rcheck/myPackage/Meta I see an entry vignette.rds. However this appears to be a binary file, so I can't make sense of it.
This is from 'writing R extensions':
At install time an HTML index for all vignettes in the package is automatically created
from the \VignetteIndexEntry statements unless a file ‘index.html’ exists in directory ‘inst/doc’. This index is linked from the HTML help index for the package. If you do supply a ‘inst/doc/index.html’ file it should contain relative links only to files under the installed ‘doc’ directory, or perhaps (not really an index) to HTML help files or to the ‘DESCRIPTION’ file.
So do I need to manually create index.html and could anyone point to an example of what this should look like?
This question appears closely related, but I do not (knowingly) have an .Rbuildignore file. This is also related, although I'm not using devtools for package creation. I have also looked at this question but am not seeing an easy answer.
Update Jul 1
For a reproducible example, the package is available here on github. Downloading and installing (e.g. with devtools::install_github() should allow this error to be reproduced.
I gather the Vignette commands need to be in the preamble, i.e. below documentclass, so that the file myVignette.Rnw should read:
\documentclass{article}
% \VignetteIndexEntry{myVignette}
% \VignetteEngine{knitr::knitr}
\usepackage[]{graphicx}
...
This seems to work fine.
The error message is from the development version of R CMD check which is currently 3.3.0. I have been using the older 'stable' version which is not the recommended way to check packages when considering submission to CRAN.
I'm still not sure of the merits of using a manual index.html file - it appears unnecessary but I will gladly change the accepted answer if anyone can throw some light on this.
This may help, or you can turn to devtools to build your package.
I am building a package in R 3.1.0 on Windows 7 32-bit (and also on a different machine running Windows 8 64bit) and I am using knitr to write vignettes using Markdown. I am hoping to publish this package on CRAN so I am using R CMD check to check that my demos, datasets and vignettes all behave properly. I keep my vignettes as .Rmd files (rather than making them outside of the package building process and stashing them in inst/doc) because they serve as extra tests on my package and aren't very big anyway.
My problem is that R CMD check fails when building my vignettes, even though if I run R CMD build and then R CMD INSTALL --build everything works out fine. Looking at the log file, it appears to be failing because it tries to evaluate code that I have explicitly told knitr NOT to evaluate. As a generic example, if I write
```{r example-chunk eval=c(1:3, 5:6), tidy=FALSE}
foo = 5
bar = 3
## don't evaluate the next line
file.show("i/dont/really/exist.csv")
## ok, start evaluating again
foobar = foo*bar
```
In a .Rmd file, running R CMD check will fail because it will try to evaluate line 4. However, the chunk will be correctly evaluated if I run R CMD build mypackage and then R CMD install --build mypackage.tar.gz (I know this because I can go to my Rlibs folder and find the flawless html vignettes in mypackage/doc. Similarly, the chunk will also be evaluated correctly I if run R CMD Sweave to build the vignette.
If you want to try this yourself, the package I am building (where I am running into the issue) is on Github: https://github.com/mkoohafkan/flowdurr-edu. You can look at raw/packagemaker.html for instructions, hopefully it's straightforward (the R code runs through the process of making the package directory, building the help files and copying some manually edited files into the package directory). R CMD check fails on all of my vignettes: when building flowdurr-datasets.Rmd, it insists on evaluating a line with a fake path even though I told it not to. When building hspf-analysis.Rmd, R CMD check insists on evaluating a line I excluded because it takes a really long time to complete (using rgenoud to fit some distribution parameters). R CMD check also fails on vignette.Rmd, but for a different reason; I purposely throw errors to show examples of what you can't do with a particular function, and while knitr doesn't have a problem with it R CMD check sure does!
EDIT: My build script was getting some hate so I made this dummy package that reproduced the problem on both of my machines. It illustrates that 1) R CMD check evaluates a line that it shouldn't, and 2) R CMD check does not support error evaluation in a vignette, even though knitr will write error output without issue.
So I guess my question is: What is it that R CMD check is doing differently from R CMD Sweave and R CMD build/install when it comes to vignette building, and is there anything I can do to make R CMD check respect knitr's 'eval' specification? Note that if I use eval=FALSE, R CMD check will respect it and everything is fine; the problem only occurs if I try selective evaluation of a chunk.
I have added vignette engines with the suffix _notangle in the knitr development version 1.6.2. For the original vignette engine knitr::foo, you can use the new engine knitr::foo_notangle to disable tangle (e.g. knitr::knitr_notangle, knitr::rmarkdown_notangle, ...).
If you do not want to wait for the next version of knitr to be on CRAN (which might take a while), you can certainly register a package vignette engine by yourself. Hint: you can make use of existing engines in tools::vignetteEngine(package = 'knitr') so you do not have to completely redefine the knitr vignette engines.
It seems that the issue is more nuanced than I originally thought, so this might not get resolved anytime soon. my workaround is to:
manually build the vignettes using R CMD Sweave
Copy the HTML outputs to inst/doc
Delete the vignettes folder (or add entries to .Rbuildignore--thanks #Ben!)
Build and check
It's not ideal, but right now it looks like the only way for my package to get through CRAN checks.
A package's .Rbuildignore looks like this:
^.*[.]Rproj.*$
^\.Rproj\.user$
^.Rhistory$
[~]
Yet R CMD check mypackage --as-cran returns:
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.Rproj.user
From reading around, it looks like this is a "feature not a bug". But how do I just prevent .Rproj.user from appearing in the package file in the first place? Or do I have a problem with my regex?
.Rbuildignore is used to ignore files when building the package. If you build the package, the files that were ignored will not be in it. I think you are probably trying to check the source instead of checking the build. Try this
R CMD build mypackage
R CMD check mypackage_1.0.tar.gz --as-cran
Writing R Extensions says:
It is strongly recommended that the final checks are run on a tar archive prepared by R CMD build.
From the Writing R Extensions Manual, I read that
As from R 2.14.0 the preferred location for the Sweave sources is the
subdirectory vignettes of the source packages, but for compatibility
with earlier versions of R, vignette sources will be looked for in
inst/doc if vignettes does not exist.
However, when I create a vignettes subdirectory of the package source, when I run devtools::check() or R CMD check I get a warning for Package vignette(s) without corresponding PDF. If I put the vignette (.Rnw and .pdf) in inst/doc the check completes without complaints. I tried looking in my library at installed packaged and did not see any directories named vignettes. Should I still use the deprecated location?
You put the .Rnw sources in vignettes/ as you did, but you missed out a critical step; don't check the source tree. The expected workflow is to build the source tarball and then check that tarball. Building the tarball will create the vignette PDF.
R CMD build ../foo/pkg
R CMD check ./pkg-0.4.tar.gz
for example will build a source package tarball from the sources in ../foo/pkg creating the .tar.gz package in the current directory with the package name and version appended. Then you run R CMD check on that source package.
If you want your vignette built for you put it in vignettes/ and build the source package. At some future date, R Core may remove the ability to build vignettes from inst/doc so go with the advised location now and avoid check the sources directly.
I had a hard time interpreting this too.
I believe the intention is that you should put the .Rnw file in vignettes/ and the PDF (suitably compacted) in inst/doc/, which technically agrees with the documentation if you read carefully enough. (That is, it says the sources should go in vignettes/. I don't see where it says in so many words that you ought to put the corresponding PDF in inst/doc/, but it doesn't not say it, and that interpretation seems to make R CMD check happy ...)
The resolution is in #GavinSimpson's answer (i.e. one is expected to build the tarball and then check it, rather than checking the source directory itself). (My two cents is that it might be best if R-core officially deprecated (and eventually removed) direct source checking rather than confusing all of us groundlings ...)