search for: r_default_packag

...I've been looking at littler's code (so this is partly a question to Dirk Eddelbuettel...): > /* We don't require() default packages upon startup; rather, we > * set up delayedAssign's instead. see autoloads(). > */ > if (setenv("R_DEFAULT_PACKAGES","NULL",1) != 0){ > perror("ERROR: couldn't set/replace R_DEFAULT_PACKAGES"); > exit(1); > } The code above happens before Rf_initEmbeddedR in littler. So I gather that just setting R_DEFAULT_PACKAGES to NULL should b...

...test.R Error in initialize(value, ...) : cannot use object of class "character" in new(): class "H5File" does not extend that class Calls: h5file -> new -> initialize -> initialize Execution halted $ /usr/lib64/R/bin/R --slave --no-restore --file=test.R [1] TRUE $ R_DEFAULT_PACKAGES= Rscript test.R [1] TRUE $ R > source('test.R') > $ R_DEFAULT_PACKAGES='datasets,utils,grDevices,graphics,stats' R > source('test.R') Error in initialize(value, ...) : cannot use object of class "character" in new(): class "H5File" does no...

...git a/src/scripts/INSTALL b/src/scripts/INSTALL index 42470c2...4c7bae9 100755 --- a/src/scripts/INSTALL +++ b/src/scripts/INSTALL @@ -9,4 +9,4 @@ while test -n "${1}"; do done ## NB: Apple's ICU needs LC_COLLATE set when R is started. -echo 'tools:::.install_packages()' | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --no-restore --slave --args ${args} +echo 'tools:::.install_packages()' | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --vanilla --slave --args ${args} diff --git a/src/scripts/REMOVE b/src/scripts/REMOVE index dcbe5bf..0be7462 100...

...######################## ############################################################################################## #############code added by gaurav yadav to install many other packages at startup############# print ("START OF CODE ADDED BY GAURAV YADAV") TEMP <- Sys.getenv("R_DEFAULT_PACKAGES") print ("R_DEFAULT_PACKAGES") print (TEMP) print ("=======") TEMP <- c(TEMP,"aplpack","approximator","apTreeshape","ArDec","arules","ash","aspace","assist","aster","asypow&...

I want to run Rcmd BATCH with R_DEFAULT_PACKAGE=base so it doesn't load any packages, but it seems to reject this argument because it does not start with a '-' or '--'. Is there a different argument that will work? Thanks. Benjamin Stabler Transportation Planning Analysis Unit Oregon Department of Transportation 555 13th...

Hi, When starting an embedded R I encounter the following issue under certain conditions: ``` Error: package or namespace load failed for ?utils? in if (.identC(class1, class2) || .identC(class2, "ANY")) TRUE else {: missing value where TRUE/FALSE needed ``` (more such errors for grDevices, graphics, and stats) And in the end: ``` Warning messages: 1: package ?utils? in

..."utils" "grDevices" "graphics" "stats" "methods" > > (plus, of course, *base*) and this can be changed by setting the option > in startup code (e.g. in ~/.Rprofile). It is initially set to the value > of the environment variable R_DEFAULT_PACKAGES if set (as a > comma-separated list). Setting R_DEFAULT_PACKAGES=NULL ensures that only > package *base* is loaded. > > Changing the set of default packages is normally used to reduce the set > for speed when scripting: in particular not using *methods*will reduce > the start-up...

Hi Dirk, Thanks for the solution. Now I know the work-arounds, but still don't quite get it. Why does R_DEFAULT_PACKAGES has anything to do with library(methods)? If library(h5) works, it should just work, not depend on an environment variable. Rscript is not consistent with R, that's my confusion. Steve 2017-12-26 20:46 GMT+08:00 Dirk Eddelbuettel <edd at debian.org>: > > On 26 December 2017 a...

...s on how to troubleshoot this problem? I have no idea > > what > > assumption we could have made. > > Note that R CMD check runs R with environment variables set as follows (at > least on my system; you can check $R_HOME/bin/check to see what it does on > yours): > > R_DEFAULT_PACKAGES= LC_COLLATE=C > > So try staring R like this: > > R_DEFAULT_PACKAGES= LC_COLLATE=C R > > And see if that reproduces the test failure. The locale setting could > affect tests of sort order, and the default package setting could > potentially affect other things. > >...

...is basic, but I can't figure out the syntax for setting options for R Commander. I'm running Linux Mint and want to increase the R Commander font sizes. I see that there are (apparently command line) options to do so. I have a desktop launcher with the following command line: sh -c 'R_DEFAULT_PACKAGES="$R_DEFAULT_PACKAGES Rcmdr" R "$@"' Can this be modified to override default font sizes? Alternatively, I've started Rcmdr from the terminal with R library(Rcmdr) but again, can't figure out where to insert the options settings to change the font size. Could...

...ot;datasets" "utils" "grDevices" "graphics" "stats" "methods" (plus, of course, *base*) and this can be changed by setting the option in startup code (e.g. in ~/.Rprofile). It is initially set to the value of the environment variable R_DEFAULT_PACKAGES if set (as a comma-separated list). Setting R_DEFAULT_PACKAGES=NULL ensures that only package *base* is loaded. Changing the set of default packages is normally used to reduce the set for speed when scripting: in particular not using *methods*will reduce the start-up time by a factor of up to tw...

...and executes it? This functionality could either be in the R source file for the package, or in the .First.lib function (decisions, decisions...)-- there wouldn't be any other functions in the package. To use the functionality, the package would just be added to the default package list in the R_DEFAULT_PACKAGES env var. If people wanted to avoid a .Renviron file, R could be invoked via R(GUI) R_DEFAULT_PACKAGES=c("stats","graphics","utils","methods","runfirst") RUNFIRST=<<whatever>> In fact I suppose you could cheat even further by includin...

Greetings, I am collaborating with developing the bigmemory package and have run in to a strange problem when we run R CMD CHECK. For some reason that isn't clear to us one of the examples crashes stating: Error: memory could not be allocated for instance of type big.matrix You can see the output on the Travis CI page at https://travis-ci.org/kaneplusplus/bigmemory where the error starts

...loaded on startup, I understand that I need to create a file .Rprofile with the path R_HOME\\etc\\.Rprofile. Again, should it be .Rprofile or Rprofile (or, is it Rprofile.site which I see is already present in my R installation)? Is the following syntax OK for specifying the environmental variable R_DEFAULT_PACKAGES = {?base?, ?datasets?,?utils?,?ggplot2?,?lattice?} How can I add, for example, ggplot2 and lattice to the list of default packages that R normally starts with? 4. If I add a .Renviron file to my working directory, will it override that in R_HOME? Or, is it the other way around? Can I add a .Rpro...

I've been working on a package that requires a shared library to be loaded. I have used the NAMESPACE file to load the library according to: http://cran.r-project.org/doc/manuals/R-exts.html#Load%20hooks <http://cran.r-project.org/doc/manuals/R-exts.html#Load%20hooks> my shared library is "excelpoi.so" hence I have added "useDynLib(excelpoi)" to my NAMESPACE file.

...les $variables$IANA_HTTP_status_code_db [1] 0 1256 $variables$IANA_URI_scheme_db [1] 1256 3458 $variables$table_of_HTTP_status_codes [1] 4714 830 $references named list() $compressed [1] TRUE > mapfile [1] "./library/tools/R/sysdata.rdx" > [1] + Stopped (SIGTSTP) R_DEFAULT_PACKAGES=NULL LC_ALL=C ./bin/R --vanilla root at x065:[/data/prj/cran/64/R-3.2.3]ls -l ./library/tools/R/sysdata.rdx -rw-r--r-- 1 root 33 193 Dec 17 16:49 ./library/tools/R/sysdata.rdx root at x065:[/data/prj/cran/64/R-3.2.3]cat ./library/tools/R/sysdata.rdx ?b```b`fbf" SH0#h^?&l...

...ocal/lib64/R/bin/INSTALL: line 455: 25001 Done ( echo "options(warn=1); invisible(.libPaths(c(\"${lib}\", .libPaths()))); .getRequiredPackages(); tools:::makeLazyLoading(\"${R_PACKAGE_NAME}\", \"${lib}\")" ) 25002 Aborted (core dumped) | R_DEFAULT_PACKAGES= LC_ALL=C "${R_EXE}" --vanilla --slave ERROR: lazy loading failed for package 'portfolio.construction' ** Removing '/usr/local/lib64/R/library/portfolio.construction' ** Restoring previous '/usr/local/lib64/R/library/portfolio.construction' [whit at linuxsvr R.pa...

On 26/12/2017 9:40 AM, Dirk Eddelbuettel wrote: > > On 26 December 2017 at 22:14, Sun Yijiang wrote: > | Thanks for the solution. Now I know the work-arounds, but still don't > | quite get it. Why does R_DEFAULT_PACKAGES has anything to do with > | library(methods)? > > Because it governs which packages are loaded by default. And while R also > loads 'methods', Rscript does not. Source of endless confusion. Mostly irrelevant correction of the jargon: that setting controls which packages a...

...k/abc/fastr/com.oracle.truffle.r.native/gnur/R-3.2.4/lib/libR.dylib Expected in: flat namespace /bin/sh: line 1: 16127 Done echo "tools:::sysdata2LazyLoadDB(\"./R/sysdata.rda\",\"../../../library/tools/R\")" 16128 Trace/BPT trap: 5 | R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R --vanilla --slave make[7]: *** [sysdata] Error 133 make[6]: *** [all] Error 2 make[5]: *** [R] Error 1 make[4]: *** [R] Error 1 make[3]: *** [R] Error 1 We always get the unknown timezone messages which I think are unrelated but I'm curious about those. Thanks...

...figure it out. > > Any thoughts on how to troubleshoot this problem? I have no idea > what > assumption we could have made. Note that R CMD check runs R with environment variables set as follows (at least on my system; you can check $R_HOME/bin/check to see what it does on yours): R_DEFAULT_PACKAGES= LC_COLLATE=C So try staring R like this: R_DEFAULT_PACKAGES= LC_COLLATE=C R And see if that reproduces the test failure. The locale setting could affect tests of sort order, and the default package setting could potentially affect other things. Dan > > Regards, > Charles >...