similar to: survival updates and testing

RHEL 6 installed R version 3.2.3 from EPEL installed Start R and use the following command, but got warnings! install.packages("rstan", dependencies = TRUE, repos = "http://cran.r-project.org/") ... g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm

Both RCurl and rstan seem to have installed now. Did the following on my RHEL6 server: [root at ping ~]# export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/ [root at ping ~]# /usr/bin/curl-config --libs -L/usr/lib64 -lcurl Now the output from your previous commands look like: [root at ping ~]# pkg-config --list-all |grep libcurl libcurl

G'day all, I guess it is still early enough in the year to wish everybody a happy and successful new year. I thought I should report that the installation of the CRAN package rstan regularly fails on my machine (a 64 bit linux box running Xubuntu 15.10). The reason being that I have the 32-bit and the 64-bit architecture of R installed, and my /tmp file is on a partition with about 1Gb

Got past my libgfortran issue ln -s /usr/lib64/libgfortran.so.3 /usr/lib/libgfortran.so Now if I could get RCurl and rstan installed. Thanks, Larry -----Original Message----- From: Tom Callaway [mailto:tcallawa at redhat.com] Sent: Friday, January 29, 2016 2:46 PM To: Patrick, Larry B [CSSM] <longplay at iastate.edu>; 'r-sig-fedora at r-project.org' <r-sig-fedora at

Hello, This problem originally surfaced as an interaction between 'brms', 'rstan' and 'Rcpp' [1]: a call to dimnames() from the 'brms' package on an object of an S4 class owned by the 'rstan' package tried to load its namespace. rstan:::.onLoad needs to load Rcpp modules, which uses load actions and reference classes. Since methods:::.findInheritedMethods

Hello, I've been trying to make LinkingTo work when the package linked to has c++ code. I've put dumb packages to illustrate this emails here ; http://addictedtor.free.fr/misc/linkingto Package A defines this C++ class: class A { public: A() ; ~A() ; SEXP hello() ; } ; Package B has this function : SEXP say_hello(){ A a ; return a.hello() ; } headers of package A are copied

Tom, First of thanks for setting up your RHEL-6 VM to help me! Until I did that link it would not install. I didn't have any libgfortran files in /usr/lib so I did that soft link. Maybe something didn't fully install or configure. I have inherited this machine from another admin and it is not a fresh installation. [root at ping /]# ls -l /usr/lib64/libgfortran* lrwxrwxrwx 1

Hello, One of our packages contains C++ code that needs to be compiled against 2 other packages. So the LinkingTo field in DESCRIPTION looks like this LinkingTo: FLCore,FLash Both packages are also in the Depends field. In R 2.6.2, first thing we noticed was that both names could not have any space between them, althoguh the example in the html version of "Writing R Extensions" does

>>>>> Ivan Krylov via R-devel >>>>> on Fri, 27 Sep 2024 13:32:27 +0300 writes: > Hello, > This problem originally surfaced as an interaction between 'brms', > 'rstan' and 'Rcpp' [1]: a call to dimnames() from the 'brms' package on > an object of an S4 class owned by the 'rstan' package tried to

I noticed that scan.c does not yet support long vectors. It was causing a problem in the rstan library (https://github.com/stan-dev/rstan/issues/530) I was able to patch base R to add long vector support. See the following gist. https://gist.github.com/aaronjg/f39e5966687ca004dab5a10e7655c648 I could not make a bugzilla account, so I am sending the patch here. [[alternative HTML version

Hello, I'm currently working on making Rcpp use the feature described here more: http://cran.r-project.org/doc/manuals/R-exts.html#Linking-to-native-routines-in-other-packages To give more context, Rcpp has for a long time built what we called "the Rcpp user library", i.e. a library we could link against user the linker. We were then producing appropriate linker flag with

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 Dirk, One side observation: r-cran debian now seems to be in Ubuntu 20.10 Universe so I don't need to add the repo any more. Here is a reproducible example that fails with the latest r-cran-rcppparallel but works when I manually install the source package: require(rstan) stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}' mod <-

I think that this problem is actually more general than just ABI versioning. The common definition of ABI refers to compiled code, but with R packages similar problems might happen (and they to happen) without any compiled code. I think the key issue is the concept of build-time dependencies. While R packages usually does not distinguish between build-time and run-time dependencies, they still do

Hi everyone, Some of you probably received the following thread from the Rcpp-devel mailing list: http://lists.r-forge.r-project.org/pipermail/rcpp-devel/2018-August/010072.html Summing up, the issue described is the following: pkg1 provides type1 in pkg1.so building on some headers. pkg2 links to pkg1 (BTW, LinkingTo is actually misleading, because it doesn't really link to it), i.e.,

I think there's one typo in your post which may confuse some readers; I've edited it inline below. My comments on the suggestion are at the bottom of the message. On 16/12/2016 5:35 AM, Kirill M?ller wrote: > Hi > > > I'd like to suggest to make R more informative when a user updates a > package A where there's at least one package B that has "LinkingTo:

Dear List, R packages may specify a "LinkingTo" attribute to specify dependencies to the source code (mainly the header files) of other packages. Unfortunately, it is not possible to also have a reference to the generated library (.dll on Windows) of the other package. So including a header file from another package to call an (exported) function will just not help. I've tried

Dear Jan, Similar functionality is available in devtools::dev_package_deps() 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

Confirmed that gcc-gfortran is installed Package gcc-gfortran-4.4.7-16.el6.x86_64 already installed and latest version What could I check next? I do not have the following installed and will get that done and tested again. libcurl-devel libidn-devel Thanks, Larry -----Original Message----- From: Tom Callaway [mailto:tcallawa at redhat.com] Sent: Wednesday, January 27, 2016

On 01/28/2016 09:07 AM, Patrick, Larry B [CSSM] wrote: > Looks to have libgfortran installed. > yum list installed | grep libgfortran > libgfortran.x86_64 4.4.7-16.el6 @rhel-x86_64-server-6 > What else could I check? > > Installed libcurl-devel and libidn-devel. > yum list installed | grep libcurl > libcurl.x86_64