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...the only form of a build-time dependency, that is completely explicit, so it is relatively easy to handle. The other frequent of build-time dependency is a function call to the other package, that happens at install time. E.g. with references or R6* classes you frequently include code like this in yourpackage: myclass <- R6::R6Class(...) and this code is evaluated at install time. So if the R6 package is updated, the installed version myclass in yourpackage is not affected at all. In fact, if the new version of R6 is not compatible with the myclass object created by the old version, then yourpacka...

On 16/12/2016 12:35 PM, Karl Millar wrote: > A couple of points: > - rebuilding dependent packages is needed if there is an ABI change, > not just an API change. For packages like Rcpp which export inline > functions or macros that might have changed, this is potentially any > change to existing functions, but for packages like Matrix, it isn't > really an issue at all

...I don't believe the "so much easier" argument that this requires a > change to base R. If you put that functionality into a package, then > the only extra effort the user would require is to install that other > package. After that, they could run > > Rscript -e "yourpackage::run_main('foo_1.1.1.tar.gz')" > > as I suggested before. This is no harder than running > > R CMD RUN foo_1.1.1.tar.gz > > The advantage of this from R Core's perspective is that you would be > developing and maintaining "yourpackage", you wouldn...

Hi all, I am trying to package a library in R 1.6.1 (Windoze XP). I have read the document "Writing R extensions" and think I have done things correctly (though apparently not). I have searched the mail archives for help to no avail. When I try to attach the library using, eg > library( libname, lib.loc=path.to.library) I get this message: Warning message: NAs introduced by

...ier to develop and test. I don't believe the "so much easier" argument that this requires a change to base R. If you put that functionality into a package, then the only extra effort the user would require is to install that other package. After that, they could run Rscript -e "yourpackage::run_main('foo_1.1.1.tar.gz')" as I suggested before. This is no harder than running R CMD RUN foo_1.1.1.tar.gz The advantage of this from R Core's perspective is that you would be developing and maintaining "yourpackage", you wouldn't be passing the burden on to...

I don't think anyone denies that you *could* make an EXE to do all that. The discussion is on *how easy* it should be to create a single file that contains an initial "main" function plus a set of bundled code (potentially as a package) and which when run will install its package code (which is contained in itself, its not in a repo), install dependencies, and run the main()

Hello, I have some troubles when building S4-class packages. All my (S4-)code works well (without building a package). When building a package, in the R prompt after checking S3 generic/method consistency Following error occurs: Fehler: Kann R Kode in Packet 'AddNoise' nicht laden (~Error: Can not load R code from package 'AddNoise') (and there are some warnings after the

...o develop and test. I don't believe the "so much easier" argument that this requires a change to base R. If you put that functionality into a package, then the only extra effort the user would require is to install that other package. After that, they could run Rscript -e "yourpackage::run_main('foo_1.1.1.tar.gz')" as I suggested before. This is no harder than running R CMD RUN foo_1.1.1.tar.gz The advantage of this from R Core's perspective is that you would be developing and maintaining "yourpackage", you wouldn't be passing the burden on...

...he "so much easier" argument that this requires a >> change to base R. If you put that functionality into a package, then >> the only extra effort the user would require is to install that other >> package. After that, they could run >> >> Rscript -e "yourpackage::run_main('foo_1.1.1.tar.gz')" >> >> as I suggested before. This is no harder than running >> >> R CMD RUN foo_1.1.1.tar.gz >> >> The advantage of this from R Core's perspective is that you would be >> developing and maintaining "...

...mmary.Rmd' using 'UTF-8' > Warning in data(skylineconfig) : data set 'skylineconfig' not found > Error in get(data(skylineconfig)) : object 'skylineconfig' not found You likely need to specify the package name, e.g. data("skylineconfig", package = "yourpackage") Also see my suggestion to use quote() to delay evaluation: > params: > configuration: !r quote(get(data(sample_analysis))) > > in the YAML will set configuration to the expression needed to get the > environment; > > eval(params$configuration) Duncan Murd...

Hi, I am building a package which contains some Java class files. I am planning to create a subdirectory "inst/Java/" in the source directory and put Java files in it, therefore after installing the package, those files will be in the "Java/" subdirectory in where the package is installed. My question is, how can I make references to those Java files in the R source files in

Dear R users, I am currently writing the documentation for my first package. I have created a short user manual using sweave/pdflatex which is distinct from the manual/summary-of-package-functions created by R CMD CHECK. I was wondering how could I seamlessly combine both documents. Thanks for your help Sebastien [[alternative HTML version deleted]]

I have posted this message on r-lang, but it is perhaps more appropriate on r-devel: --- Hello, I'm puzzled by a problem with call to diag(), rowSums(), rownames() on objects of class "dgtMatrix", created by sparseMatrix() or spMatrix(). I use Matrix 0.999375-30. The weird thing is that I don't encounter any problem when I use this functions on the R prompt, or

Dear All, I have built a package which has a data.frame "annotIndex.rda in its "data" folder. I am using this data frame within two functions in my package. Though my package works fine, yet when I do a R CMD check to my package I get the following two notes get.affy.ensembl: no visible binding

Hello! I am truing to compile an R-package having c-code. I put foo.c in src/ folder and useDynLib("foo") in NAMESPACE file. When trying R CMD check, I got an error message that shared object 'foo' is not found. Then I did R CMD SHLIB foo.c first. However, after that, I got warnings from R CMD check that there is an object file in /src folder. Even worse is if I run R CMD

Dear List, I am working on moving some Rmarkdown reports into the vignettes folder of a package. While I was able to solve to problem of parametrized reports in vignettes folder thanks to your invaluable help (Thank you), I am now struggling with the following problem. One of the reports which I am moving to vignettes includes the following code : ```{r} child_docs <-

...o do that is to put them > in a new directory called "inst/children", which will be installed to > "children" when your package is installed. Then the vignette can find the > file as > > system.file(file.path("children", child_docs), package = "yourpackage") > > You could also put them in the "vignettes" directory, but there are special > rules for how files there are installed or not, so I'd recommend against it. > > Duncan Murdoch -- Witold Eryk Wolski

...' >> Warning in data(skylineconfig) : data set 'skylineconfig' not found >> Error in get(data(skylineconfig)) : object 'skylineconfig' not found > > > You likely need to specify the package name, e.g. > > data("skylineconfig", package = "yourpackage") > > Also see my suggestion to use quote() to delay evaluation: > > >> params: >> configuration: !r quote(get(data(sample_analysis))) >> >> in the YAML will set configuration to the expression needed to get the >> environment; >> >>...

...package. One way to do that is to put them in a new directory called "inst/children", which will be installed to "children" when your package is installed. Then the vignette can find the file as system.file(file.path("children", child_docs), package = "yourpackage") You could also put them in the "vignettes" directory, but there are special rules for how files there are installed or not, so I'd recommend against it. Duncan Murdoch

Hi Dear R-users: I am building a R package and would like to create a generic variance function. Here is how I did var=function(x,...) { UseMethod("var") } I wrote a Rd file, put the R code in the right directory, and named var, var.default in the namespace. However, once I typed rcmd check , it gave me an error in S3-generic step. However, that error would not occur for mean and