similar to: How to remove packages from the active working window

Hi, I need to link mypackage to 2 other packages so I can call some C functions defined in these 2 packages from mine. I've tried Depends: packageA, packageB LinkingTo: packageA, packageB as suggested by the "5.4 Registering native routines" section of the "Writing R Extensions" manual but then only packageA is seen at compilation time (gcc is called with

Hi, In the case where install.packages("packageA") also needs to install required package "packageB", then what is passed thru the 'configure.args' argument seems to be lost when it's the turn of packageA to be installed (the last package to get installed). This is not easy to reproduce but let's say you have the graphviz libraries installed on your system,

Hi, I developed a package that requires 5 other packages. I was wondering if anyone knows how can I automatically download and install the required packages during the installation of my new package. My idea is to make this process easier to the final user. All the required packages are under bioconductor source but I don't know where I can include the code to download and install them.

I have been using batch mode successfully. I try this using cygwin on a PC with 3.0.4 version of rsync. The two PackageOlder dirs are identical cygwin> diff -r /home/bill/tmp/PackageB /home/bill/PackageB cygwin> rsync -vv --only-write-batch=/Temp/changeAtoB.rsync -rptO -L --delete-delay devserver::RT/PackageB/ /home/bill/tmp/PackageA opening tcp connection to devserver port 873 sending

Hi Duncan, Many thanks (yet again). With the hint given by your earlier email (viz that currently loadNamespace expects a 3rd component called name in the list that is used for the versionCheck argument) I had another look at what was going on with my toy examples yesterday evening. I'm still working on my issue, but thus far I have: 1) Confirmed that internal calls to loadNamespace

Hi although the background is that it happened on an hpc cluster, this question does *not* concern hpc computing with R. I was using R on a cluster and had to install several packages in my home directory. Now the head node was migrated to new hardware (new install as well) and many dependencies for my in $HOME installed packages, which were present on the old head, are missing on the new head.

Hi, SETUP: Consider three packages PkgA, PkgB and PkgC. PkgA defines a generic function foo() and exports it; export(foo) PkgB imports PkgA::foo() and re-exports it; importFrom(PkgA, foo) export(foo) PkgC imports everything from PkgA and PkgB: imports(PkgA, PkgB) PROBLEM: Loading or attaching the namespace of PkgC will generate a warning: replacing previous import by

Hi, I have a problem - looking for advice. I have a source code file with two functions which are compiled into a .bc file. When the bitcode file is loaded, I can dump the module and see the two functions: ... ; Materializable ; Function Attrs: noinline nounwind uwtable define void @matmul(double*, double*, double*, i32, i32, i32) #0 {} ; Materializable ; Function Attrs: noinline nounwind

Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch (to the base class method). The attached package reproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A",

Dear All, I am trying to do the following, and could use some hints. Suppose I have a package called pkgA. pkgA exposes an API that includes setting some options, e.g. pkgA works with color palettes, and the user of the package can define new palettes. pkgA provides an API to manipulate these palettes, including defining them. pkgA is intended to be used in other packages, e.g. in pkgB1 and

I was wondering: are the downstream dependencies of a package rebuilt when a package is updated on CRAN? (I'm referring to the binary packages, of course.) The reason I ask is because there are cases where this can cause problems. Suppose that when pkgB is built, it calls pkgA::makeClosure(), which returns a closure that refers to a function in pkgA. Suppose this code is in pkgA 1.0:

>>>>> Martin Morgan <mtmorgan at fredhutch.org> >>>>> on Mon, 11 May 2015 10:18:07 -0700 writes: > On 05/10/2015 08:19 AM, Martin Morgan wrote: >> Loading an S4 object from a file without first loading the library sometimes (?, >> the example below and actual example involves a virtual base class and the show >> generic)

I have recently installed R on DEC Alpha OSF 5.1. The first regression test (reg-test-1.R) failed with an unresolved symbol in lapack.so: 2246839:/data/h1/bifdev/apps/wga/R-1.9.1/bin/R.bin: /sbin/loader: Fatal Error: call to unresolved symbol from /data/h1/bifdev/apps/wga/R-1.9.1/modules/lapack.so (pc=0x3ffbfe22b60) Further investigation has revealed that there is NO problem with lapack.so. The

I have recently installed R on DEC Alpha OSF 5.1. The first regression test (reg-test-1.R) failed with an unresolved symbol in lapack.so: 2246839:/data/h1/bifdev/apps/wga/R-1.9.1/bin/R.bin: /sbin/loader: Fatal Error: call to unresolved symbol from /data/h1/bifdev/apps/wga/R-1.9.1/modules/lapack.so (pc=0x3ffbfe22b60) Further investigation has revealed that there is NO problem with lapack.so. The

I?m following along a few tutorials on the web and trying to implement my own example, but I must be missing something because I can?t get has_many or belongs_to to work like I expected. now I have watched all the videos and made a cookbook several times with different interfaces. what I''m looking for is *not* a code snippet to solve something (because I already have that),

Dear list, It seems that a package (pkgB) using another package (pkgA) with S4 generics formed by taking existing functions (for example 'plot') must not import the existing functions ('plot') in its namespace to avoid the warning "replacing previous import: plot". Suppose we use the simple 'import' directive in the name space of pkgB. pkgA and pkgB files would

pkgA's NAMESPACE has importFrom(graphics, plot) exportClasses("A") exportMethods("plot") R/foo.R has setClass("A") setMethod("plot", "A", function(x, y, ...) {}) During R CMD INSTALL pkgA_1.0.tar.gz we are told ** preparing package for lazy loading Creating a generic function for 'plot' from package

In the documentation the closed thing I see to an explanation of this is that ?detach says "Unloading some namespaces has undesirable side effects" Can anyone explain why unloading tseries will load zoo? I don't think this behavior is specific to tseries, it's just an example. I realize one would not usually unload something that is not loaded, but I would expect it to do

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

Dear all, Consider this code: >library("data.table") >unloadNamespace('data.table') It produces some warnings Warning in FUN(X[[1L]], ...) : Created a package name, ‘2013-10-29 17:05:51’, when none found Warning in FUN(X[[1L]], ...) : Created a package name, ‘2013-10-29 17:05:51’, when none found ... The warning is produced by the getPackageName() function. e.g.