Re: [Rd] R-forge, package dependencies
Nick Sabbe nick.sa...@ugent.be on Tue, 15 Jan 2013 21:34:52 +0100 writes: I have exactly the same issue with a pair of my packages on R-Forge. I've already notified Stefan, but I mentioned it wasn't urgent for me :) It must have something to do with the R check using a different environment than the build... notably when using '--as-cran' I think; this looks like a pretty infelicitous decision to me: E.g. I can no longer use --as-cran for checking our copula package (on my own computer), as that suggests Rmpfr and gmp and these depend on the corresponding external C libraries (mpfr gmp) and these rely on LD_LIBRARY_PATH and that now fails to be looked at in such circumstances. To me this somewhat recent change looks like something that should be re-considered on the R side.. Martin So good hunting, Stefan! indeed... Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Uwe Ligges Sent: dinsdag 15 januari 2013 21:09 To: Thomas Lumley Cc: Stefan Theussl; R-devel Subject: Re: [Rd] R-forge, package dependencies On 15.01.2013 20:47, Thomas Lumley wrote: I have a project on R-forge (sqlsurvey.r-forge.r-project.org) with two packages, RMonetDB and sqlsurvey. At the moment, sqlsurvey is listed as failing to build. The error is on the Linux package check, which says that RMonetDB is not available: * checking package dependencies ... ERROR Package required but not available: 'RMonetDB' RMonetDB has built successfully: r-forge lists its status as 'current', with Linux, Windows, and Mac packages available for download. The package check for sqlsurvey on Windows and Mac finds RMonetDB without any problems, it's just on Linux that it appears to be unavailable. Any suggestions for how to fix this? I've tried uploading a new version of RMonetDB, but the situation didn't change: it built successfully, but the Linux check of sqlsurvey still couldn't find it. I think you have to ask Stefan to check the details. Best, Uwe -thomas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-forge, package dependencies
Hi, the same error was happen to me as well. it doesn't have problem with mac and windows but there is package dependencies with Linux platform. this is something i don't get a solution yet. so what I've done is, I simply check on win-builder for machine dependencies and on my local machine as well, then I built and submitted it to cran using ftp. But still the issue for Linux and r forge is what i can't get a solution. Regards, Michael On Wed, Jan 16, 2013 at 9:31 AM, Martin Maechler maech...@stat.math.ethz.ch wrote: Nick Sabbe nick.sa...@ugent.be on Tue, 15 Jan 2013 21:34:52 +0100 writes: I have exactly the same issue with a pair of my packages on R-Forge. I've already notified Stefan, but I mentioned it wasn't urgent for me :) It must have something to do with the R check using a different environment than the build... notably when using '--as-cran' I think; this looks like a pretty infelicitous decision to me: E.g. I can no longer use --as-cran for checking our copula package (on my own computer), as that suggests Rmpfr and gmp and these depend on the corresponding external C libraries (mpfr gmp) and these rely on LD_LIBRARY_PATH and that now fails to be looked at in such circumstances. To me this somewhat recent change looks like something that should be re-considered on the R side.. Martin So good hunting, Stefan! indeed... Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Uwe Ligges Sent: dinsdag 15 januari 2013 21:09 To: Thomas Lumley Cc: Stefan Theussl; R-devel Subject: Re: [Rd] R-forge, package dependencies On 15.01.2013 20:47, Thomas Lumley wrote: I have a project on R-forge (sqlsurvey.r-forge.r-project.org) with two packages, RMonetDB and sqlsurvey. At the moment, sqlsurvey is listed as failing to build. The error is on the Linux package check, which says that RMonetDB is not available: * checking package dependencies ... ERROR Package required but not available: 'RMonetDB' RMonetDB has built successfully: r-forge lists its status as 'current', with Linux, Windows, and Mac packages available for download. The package check for sqlsurvey on Windows and Mac finds RMonetDB without any problems, it's just on Linux that it appears to be unavailable. Any suggestions for how to fix this? I've tried uploading a new version of RMonetDB, but the situation didn't change: it built successfully, but the Linux check of sqlsurvey still couldn't find it. I think you have to ask Stefan to check the details. Best, Uwe -thomas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] How to call Java main method using rJava package?
Hi,
I am trying to integrate my Java program with R using rJava package. I want
to execute the whole Java program from R. The main() method in my Java code
calls all the other defined methods. So, I guess I have to call the main()
method in .jcall.
An example Java code:
*class A {
public static int mySum(int x, int y) {
return x+y;
}
public static void main (String[] arg) {
System.out.println(The sum is + mySum(2, 4));
}
}*
I can do the following to call the mySum() method:
*.jcall(obj, I, mySum, as.integer(2), as.integer(4))*
This will give the output *6*.
But can some one explain me that how exactly I can execute this program to
print *The sum is 6* from R? OR how can I call the main method?
I am a beginner in R.
Thanks,
Gaurav
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[Rd] Small clarification to R-exts, questions on ptr_do_selectlist
Hi,
1. I suggest adding the following piece of advice at the end of the section
describing R_getEmbeddingDllInfo() (currently 8.1.3) in R-exts.texi:
---
In order to call registered symbols of the embedding application from a
package, you have to specify @code{PACKAGE = (embedding)} in
@code{.C}, @code{.Call}, etc.
---
2. Section 8.1.2 of R-exts.text (Setting R callbacks) has a new line These
callbacks should never be changed in a running R session (and hence cannot be
called from an extension package). I had a bit of difficulty understanding
what These refers to. I believe it's meant to refer to the above
callbacks, only, and I suggest using that wording for easier reading.
3. While reading the sources, trying to understand how to make use of
prt_do_selectlist, it seems that this is not actually used to
utils::select.list(), unless
(.Platform$OS.type == windows || .Platform$GUI == AQUA)
Is this intended?
In fact, from reading src/library/utils/src/stubs.c, it looks like
ptr_do_selectlist (and ptr_do_data(entry|viewer), ptr_R_(add|load|
save)history) is ignored on Windows, although - from a naive POV - it would
seem easy enough to make it functional across platforms(*).
Regards
Thomas
(*) E.g. changing the selectlist stub to:
--
SEXP selectlist(SEXP call, SEXP op, SEXP args, SEXP env)
{
if(ptr_do_selectlist) return ptr_do_selectlist(call, op, CDR(args), env);
#ifdef Win32
return Win_selectlist(CDR(args));
#else
return R_NilValue;
#endif
}
--
and removing the Windows specific stub, earlier in the file.
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[Rd] Trouble building package using R in development
Dear List, I'm having considerable trouble setting up my environment (Linux, Fedora 16, Bash) to build and check packages under R Under Development (r61660). I'm doing this to better get a handle on difference in the output from running checks on examples in one of my packages. Note I compiled R Under Development myself The problem I am now having is whenever I try to build my analogue package using R Under Development, R complains about a dependency having been built before R 3.0.0. I obviously don't have my environment variables set correctly, but I don't see why or how R is finding my daily-use package library; if anything I would have expected it to fail with a missing dependency. If I start Rdevel with --vanilla (to mimic Rdevel CMD build) I see: .libPaths() [1] /home/gavin/R/devlibs /home/gavin/R/devel/build/library the first entry there is because I have temporarily set R_LIBS to that directory via export R_LIBS=/home/gavin/R/devlibs. From there we see I have versions of the dependencies installed in this library and they are built with 3.0.0: installed.packages(~/R/devlibs/)[, Built, drop = FALSE] Built analogue 3.0.0 ctv 3.0.0 permute 3.0.0 princurve 3.0.0 rgl 3.0.0 scatterplot3d 3.0.0 vegan 3.0.0 Note that there are no other versions of vegan inadvertently installed to the build directory for R Under Development. Following advice in Writing R Extensions I have also created ~/build.Renviron and ~/check.Renviron and as these are non-standard I also followed the advice to set R_BUILD_ENVIRON and R_CHECK_ENVIRON again temporarily via export: $ cat $R_CHECK_ENVIRON R_LIBS=/home/gavin/R/devlibs $ cat $R_BUILD_ENVIRON R_LIBS=/home/gavin/R/devlibs Yet still I get errors building analogue: $ Rdevel CMD build ../analogue/pkg/ * checking for file ‘../analogue/pkg/DESCRIPTION’ ... OK * preparing ‘analogue’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes --- * installing *source* package ‘analogue’ ... ** libs gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distx.c -o c_distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distxy.c -o c_distxy.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c distx.c -o distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c distxy.c -o distxy.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c wastats.c -o wastats.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o analogue.so c_distx.o c_distxy.o distx.o distxy.o wastats.o installing to /tmp/Rtmpctxbtv/Rinst30e3f762569/analogue/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error : package ‘vegan’ was built before R 3.0.0: please re-install it ERROR: lazy loading failed for package ‘analogue’ * removing ‘/tmp/Rtmpctxbtv/Rinst30e3f762569/analogue’ --- ERROR: package installation failed Can anyone suggest where to go from here? TIA Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to call Java main method using rJava package?
On Jan 16, 2013, at 7:32 AM, Gaurav Dasgupta wrote:
Hi,
I am trying to integrate my Java program with R using rJava package. I want
to execute the whole Java program from R. The main() method in my Java code
calls all the other defined methods. So, I guess I have to call the main()
method in .jcall.
An example Java code:
*class A {
public static int mySum(int x, int y) {
return x+y;
}
public static void main (String[] arg) {
System.out.println(The sum is + mySum(2, 4));
}
}*
I can do the following to call the mySum() method:
*.jcall(obj, I, mySum, as.integer(2), as.integer(4))*
This will give the output *6*.
But can some one explain me that how exactly I can execute this program to
print *The sum is 6* from R? OR how can I call the main method?
.jcall(A,V,main,.jarray(list(), java/lang/String)
But note that System.out is sent to stdout by Java so it won't output in the R
console as R output so you should really avoid it.
You may consider using the stats-rosuda-devel mailing list for rJava questions.
Cheers,
Simon
I am a beginner in R.
Thanks,
Gaurav
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Re: [Rd] Trouble building package using R in development
As a follow-up, shortly after I clicked send I decided to do something silly and rename my ~/.Renviron (which set R_LIBS too). Silly because the Writing R Extensions (WRE) manual says that these startup files are not read as R is invoked with --vanilla. Once I renamed ~/.Renviron so it was not being read I was able to build the package using R Under Development following the remaining instructions in the WRE note [1] So I do wonder if I have misunderstood the note in WRE or if there is some other issue here? Starting R --vanilla with R Under Development wasn't reading ~/.Renviron, and by renaming ~/.Renviron that I was able to build the package indicates that this file was implicated in the problem I described. Is it intentional that R CMD build reads ~/.Renviron ? If it is, then WRE should ideally clarify this or make it explicit. If it wasn't supposed to be read, is there a bug here? All the best, Gavin [1] http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-and-building-packages On Wed, 2013-01-16 at 16:05 +0100, Gavin Simpson wrote: Dear List, I'm having considerable trouble setting up my environment (Linux, Fedora 16, Bash) to build and check packages under R Under Development (r61660). I'm doing this to better get a handle on difference in the output from running checks on examples in one of my packages. Note I compiled R Under Development myself The problem I am now having is whenever I try to build my analogue package using R Under Development, R complains about a dependency having been built before R 3.0.0. I obviously don't have my environment variables set correctly, but I don't see why or how R is finding my daily-use package library; if anything I would have expected it to fail with a missing dependency. If I start Rdevel with --vanilla (to mimic Rdevel CMD build) I see: .libPaths() [1] /home/gavin/R/devlibs /home/gavin/R/devel/build/library the first entry there is because I have temporarily set R_LIBS to that directory via export R_LIBS=/home/gavin/R/devlibs. From there we see I have versions of the dependencies installed in this library and they are built with 3.0.0: installed.packages(~/R/devlibs/)[, Built, drop = FALSE] Built analogue 3.0.0 ctv 3.0.0 permute 3.0.0 princurve 3.0.0 rgl 3.0.0 scatterplot3d 3.0.0 vegan 3.0.0 Note that there are no other versions of vegan inadvertently installed to the build directory for R Under Development. Following advice in Writing R Extensions I have also created ~/build.Renviron and ~/check.Renviron and as these are non-standard I also followed the advice to set R_BUILD_ENVIRON and R_CHECK_ENVIRON again temporarily via export: $ cat $R_CHECK_ENVIRON R_LIBS=/home/gavin/R/devlibs $ cat $R_BUILD_ENVIRON R_LIBS=/home/gavin/R/devlibs Yet still I get errors building analogue: $ Rdevel CMD build ../analogue/pkg/ * checking for file ‘../analogue/pkg/DESCRIPTION’ ... OK * preparing ‘analogue’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes --- * installing *source* package ‘analogue’ ... ** libs gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distx.c -o c_distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distxy.c -o c_distxy.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c distx.c -o distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c distxy.c -o distxy.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c wastats.c -o wastats.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o analogue.so c_distx.o c_distxy.o distx.o distxy.o wastats.o installing to /tmp/Rtmpctxbtv/Rinst30e3f762569/analogue/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error : package ‘vegan’ was built before R 3.0.0: please re-install it ERROR: lazy loading failed for package
[Rd] Declaring/importing non-exported functions [car] in another package
A new function in my heplots package wants to use a non-exported utility function in the car package, df.terms, but this depends on other non-exported functions. From the Writing R extensions manual, I thought I could do this via (in my NAMESPACE) importFrom(car, car:::df.terms, car:::df.terms.default, car:::is.aliased) but I get: ** preparing package for lazy loading Error : objects 'car:::df.terms', 'car:::df.terms.default', 'car:::is.aliased' are not exported by 'namespace:car' ERROR: lazy loading failed for package 'heplots' \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? 2. Is my only alternative to copy these functions to my package, also unexported? thx, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Declaring/importing non-exported functions [car] in another package
On 13-01-16 11:25 AM, Michael Friendly wrote: A new function in my heplots package wants to use a non-exported utility function in the car package, df.terms, but this depends on other non-exported functions. From the Writing R extensions manual, I thought I could do this via (in my NAMESPACE) importFrom(car, car:::df.terms, car:::df.terms.default, car:::is.aliased) but I get: ** preparing package for lazy loading Error : objects 'car:::df.terms', 'car:::df.terms.default', 'car:::is.aliased' are not exported by 'namespace:car' ERROR: lazy loading failed for package 'heplots' \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? I think you misread the manual. It is talking about ways to access functions other than by using importFrom. You can use car:::df.terms in your functions. 2. Is my only alternative to copy these functions to my package, also unexported? Using car:::df.terms explicitly is another option. Another possibility is for the car maintainer (John Fox) to export that function from car. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Declaring/importing non-exported functions [car] in another package
On 1/16/2013 11:40 AM, Duncan Murdoch wrote: \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? I think you misread the manual. It is talking about ways to access functions other than by using importFrom. You can use car:::df.terms in your functions. Thanks for the clarification, but I blame the manual. Could I suggest a change in the manual to make this clearer: Using |foo:::f| directly in a function instead of |foo::f| allows access to unexported objects (rather than in importsFrom()). ... -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Trouble building package using R in development
On Wed, Jan 16, 2013 at 7:25 AM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: As a follow-up, shortly after I clicked send I decided to do something silly and rename my ~/.Renviron (which set R_LIBS too). Silly because the Writing R Extensions (WRE) manual says that these startup files are not read as R is invoked with --vanilla. Once I renamed ~/.Renviron so it was not being read I was able to build the package using R Under Development following the remaining instructions in the WRE note [1] So I do wonder if I have misunderstood the note in WRE or if there is some other issue here? Starting R --vanilla with R Under Development wasn't reading ~/.Renviron, and by renaming ~/.Renviron that I was able to build the package indicates that this file was implicated in the problem I described. Is it intentional that R CMD build reads ~/.Renviron ? If it is, then WRE should ideally clarify this or make it explicit. If it wasn't supposed to be read, is there a bug here? FYI, related posts: * Rd thread 'R devel [and R 2.14.1 patched]: R CMD build now sources ~/.Rprofile' on Feb 23, 2012 [https://stat.ethz.ch/pipermail/r-devel/2012-February/063365.html] * Rd thread 'R CMD build/check on Windows 7' on Jul 17, 2012 [https://stat.ethz.ch/pipermail/r-devel/2012-July/064427.html] To circumvent this, I check using: R --no-init-file CMD check foo_1.0.tar.gz /Henrik All the best, Gavin [1] http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-and-building-packages On Wed, 2013-01-16 at 16:05 +0100, Gavin Simpson wrote: Dear List, I'm having considerable trouble setting up my environment (Linux, Fedora 16, Bash) to build and check packages under R Under Development (r61660). I'm doing this to better get a handle on difference in the output from running checks on examples in one of my packages. Note I compiled R Under Development myself The problem I am now having is whenever I try to build my analogue package using R Under Development, R complains about a dependency having been built before R 3.0.0. I obviously don't have my environment variables set correctly, but I don't see why or how R is finding my daily-use package library; if anything I would have expected it to fail with a missing dependency. If I start Rdevel with --vanilla (to mimic Rdevel CMD build) I see: .libPaths() [1] /home/gavin/R/devlibs /home/gavin/R/devel/build/library the first entry there is because I have temporarily set R_LIBS to that directory via export R_LIBS=/home/gavin/R/devlibs. From there we see I have versions of the dependencies installed in this library and they are built with 3.0.0: installed.packages(~/R/devlibs/)[, Built, drop = FALSE] Built analogue 3.0.0 ctv 3.0.0 permute 3.0.0 princurve 3.0.0 rgl 3.0.0 scatterplot3d 3.0.0 vegan 3.0.0 Note that there are no other versions of vegan inadvertently installed to the build directory for R Under Development. Following advice in Writing R Extensions I have also created ~/build.Renviron and ~/check.Renviron and as these are non-standard I also followed the advice to set R_BUILD_ENVIRON and R_CHECK_ENVIRON again temporarily via export: $ cat $R_CHECK_ENVIRON R_LIBS=/home/gavin/R/devlibs $ cat $R_BUILD_ENVIRON R_LIBS=/home/gavin/R/devlibs Yet still I get errors building analogue: $ Rdevel CMD build ../analogue/pkg/ * checking for file ‘../analogue/pkg/DESCRIPTION’ ... OK * preparing ‘analogue’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes --- * installing *source* package ‘analogue’ ... ** libs gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distx.c -o c_distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distxy.c -o c_distxy.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c distx.c -o distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c distxy.c -o distxy.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
Re: [Rd] Trouble building package using R in development
On Wed, Jan 16, 2013 at 8:59 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Wed, Jan 16, 2013 at 7:25 AM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: As a follow-up, shortly after I clicked send I decided to do something silly and rename my ~/.Renviron (which set R_LIBS too). Silly because the Writing R Extensions (WRE) manual says that these startup files are not read as R is invoked with --vanilla. Once I renamed ~/.Renviron so it was not being read I was able to build the package using R Under Development following the remaining instructions in the WRE note [1] So I do wonder if I have misunderstood the note in WRE or if there is some other issue here? Starting R --vanilla with R Under Development wasn't reading ~/.Renviron, and by renaming ~/.Renviron that I was able to build the package indicates that this file was implicated in the problem I described. Is it intentional that R CMD build reads ~/.Renviron ? If it is, then WRE should ideally clarify this or make it explicit. If it wasn't supposed to be read, is there a bug here? FYI, related posts: * Rd thread 'R devel [and R 2.14.1 patched]: R CMD build now sources ~/.Rprofile' on Feb 23, 2012 [https://stat.ethz.ch/pipermail/r-devel/2012-February/063365.html] * Rd thread 'R CMD build/check on Windows 7' on Jul 17, 2012 [https://stat.ethz.ch/pipermail/r-devel/2012-July/064427.html] To circumvent this, I check using: R --no-init-file CMD check foo_1.0.tar.gz Should have clarified that in your case you need to add '--no-environ'. /Henrik /Henrik All the best, Gavin [1] http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-and-building-packages On Wed, 2013-01-16 at 16:05 +0100, Gavin Simpson wrote: Dear List, I'm having considerable trouble setting up my environment (Linux, Fedora 16, Bash) to build and check packages under R Under Development (r61660). I'm doing this to better get a handle on difference in the output from running checks on examples in one of my packages. Note I compiled R Under Development myself The problem I am now having is whenever I try to build my analogue package using R Under Development, R complains about a dependency having been built before R 3.0.0. I obviously don't have my environment variables set correctly, but I don't see why or how R is finding my daily-use package library; if anything I would have expected it to fail with a missing dependency. If I start Rdevel with --vanilla (to mimic Rdevel CMD build) I see: .libPaths() [1] /home/gavin/R/devlibs /home/gavin/R/devel/build/library the first entry there is because I have temporarily set R_LIBS to that directory via export R_LIBS=/home/gavin/R/devlibs. From there we see I have versions of the dependencies installed in this library and they are built with 3.0.0: installed.packages(~/R/devlibs/)[, Built, drop = FALSE] Built analogue 3.0.0 ctv 3.0.0 permute 3.0.0 princurve 3.0.0 rgl 3.0.0 scatterplot3d 3.0.0 vegan 3.0.0 Note that there are no other versions of vegan inadvertently installed to the build directory for R Under Development. Following advice in Writing R Extensions I have also created ~/build.Renviron and ~/check.Renviron and as these are non-standard I also followed the advice to set R_BUILD_ENVIRON and R_CHECK_ENVIRON again temporarily via export: $ cat $R_CHECK_ENVIRON R_LIBS=/home/gavin/R/devlibs $ cat $R_BUILD_ENVIRON R_LIBS=/home/gavin/R/devlibs Yet still I get errors building analogue: $ Rdevel CMD build ../analogue/pkg/ * checking for file ‘../analogue/pkg/DESCRIPTION’ ... OK * preparing ‘analogue’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes --- * installing *source* package ‘analogue’ ... ** libs gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distx.c -o c_distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c c_distxy.c -o c_distxy.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c distx.c -o distx.o gcc -std=gnu99 -I/home/gavin/R/devel/build/include -DNDEBUG -I/usr/local/include-fpic -g -O2 -pipe -m64 -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -march=core2 -fasynchronous-unwind-tables -c
Re: [Rd] Declaring/importing non-exported functions [car] in another package
On 1/16/2013 11:40 AM, Duncan Murdoch wrote:
2. Is my only alternative to copy these functions to my package, also
unexported?
Using car:::df.terms explicitly is another option.
Another possibility is for the car maintainer (John Fox) to export
that function from car.
Hmm. It turns out that this is a bit more complicated, since
car::df.terms is an S3 generic,
relying on car:::df.terms.default().
In my function, I am now using car::: explicitly--
# determine size of intervals [perhaps need importFrom(car,
car:::df.terms, ...) in NAMESPACE?]
if(is.null(df)) {
df - if (Scheffe) sum(car:::df.terms(object)) else 2
}
However, when I removed the definitions of the subsidiary
df.terms.default from my package, R CMD check
complains bitterly:
coefplot(mod, add=TRUE, Scheffe=TRUE, fill=TRUE)
Error in UseMethod(df.terms) :
no applicable method for 'df.terms' applied to an object of class
c('mlm', 'lm')
Calls: coefplot - coefplot.mlm - Anonymous
Execution halted
So, the semantics of importFrom() do not allow non-exported functions (I
still wonder why), and my only direct option is to
copy these functions to my package.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Declaring/importing non-exported functions [car] in another package
Dear Duncan and Michael, My initial reaction is that I'd rather not export these functions from the car package since the package already has many exported functions and the functions in question perform low-level operations that won't be of interest to end users. I recognize, however, the functions (and possibly some others) may be useful in other packages, such as heplots, so I'll think about this some more. Following up on Michael's subsequent message in this thread, I find the current text in Sec. 1.6.1 (Specifying imports and exports) of Writing R Extensions reasonably clear. Best, John On Wed, 16 Jan 2013 11:40:37 -0500 Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-01-16 11:25 AM, Michael Friendly wrote: A new function in my heplots package wants to use a non-exported utility function in the car package, df.terms, but this depends on other non-exported functions. From the Writing R extensions manual, I thought I could do this via (in my NAMESPACE) importFrom(car, car:::df.terms, car:::df.terms.default, car:::is.aliased) but I get: ** preparing package for lazy loading Error : objects 'car:::df.terms', 'car:::df.terms.default', 'car:::is.aliased' are not exported by 'namespace:car' ERROR: lazy loading failed for package 'heplots' \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? I think you misread the manual. It is talking about ways to access functions other than by using importFrom. You can use car:::df.terms in your functions. 2. Is my only alternative to copy these functions to my package, also unexported? Using car:::df.terms explicitly is another option. Another possibility is for the car maintainer (John Fox) to export that function from car. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Declaring/importing non-exported functions [car] in another package
On 1/16/2013 12:26 PM, John Fox wrote: Dear Duncan and Michael, My initial reaction is that I'd rather not export these functions from the car package since the package already has many exported functions and the functions in question perform low-level operations that won't be of interest to end users. I recognize, however, the functions (and possibly some others) may be useful in other packages, such as heplots, so I'll think about this some more. This is why I wrote directly to R-devel rather than to you. It is low-level, and doesn't need to be exported. OTOH, it provides an elegant way to provide Sheffe-type intervals ellipses as you do in car::confidenceEllipse, which I copied. best, -Michael Following up on Michael's subsequent message in this thread, I find the current text in Sec. 1.6.1 (Specifying imports and exports) of Writing R Extensions reasonably clear. Best, John On Wed, 16 Jan 2013 11:40:37 -0500 Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-01-16 11:25 AM, Michael Friendly wrote: A new function in my heplots package wants to use a non-exported utility function in the car package, df.terms, but this depends on other non-exported functions. From the Writing R extensions manual, I thought I could do this via (in my NAMESPACE) importFrom(car, car:::df.terms, car:::df.terms.default, car:::is.aliased) but I get: ** preparing package for lazy loading Error : objects 'car:::df.terms', 'car:::df.terms.default', 'car:::is.aliased' are not exported by 'namespace:car' ERROR: lazy loading failed for package 'heplots' \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? I think you misread the manual. It is talking about ways to access functions other than by using importFrom. You can use car:::df.terms in your functions. 2. Is my only alternative to copy these functions to my package, also unexported? Using car:::df.terms explicitly is another option. Another possibility is for the car maintainer (John Fox) to export that function from car. Duncan Murdoch -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check not reading R_LIBS from ~/.R/check.Renviron
Dear List, Further to my earlier email, I note that, for me at least, R CMD check is *not* reading R_LIBS from ~/.R/check.Renviron on R 2.15.2 patched (r61228) and R Under Development (r61660). The only way I can get R CMD check to look for packages in a user-supplied library is by explicitly exporting R_LIBS set to the relevant directory. R CMD build *does* read R_LIBS from ~/.R/build.Renviron for the same versions of R on the same Fedora 16 laptop. So I am in the strange situation of being able to build but not check a source package having followed the instructions in Writing R Extensions. I have tried exporting R_CHECK_ENVIRON via export R_CHECK_ENVIRON=/home/gavin/.R/check.Renviron and that doesn't work either. ~/.R/check.Renviron contains: R_LIBS=/home/gavin/R/libs/ #R_LIBS=/home/gavin/R/devlibs/ Anyone suggest how/where I am going wrong? More complete system info follows below. TIA Gavin sessionInfo() R version 2.15.2 Patched (2012-12-05 r61228) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=CLC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base sessionInfo() R Under development (unstable) (2013-01-16 r61660) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=CLC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Trouble building package using R in development
To circumvent this, I check using: R --no-init-file CMD check foo_1.0.tar.gz In devtools, we take considerable care to match the R you're running with the R you're checking in, so we also set the following environmental variables: env - c( LC_ALL = C, R_LIBS = paste(.libPaths(), collapse = .Platform$path.sep), CYGWIN = nodosfilewarning, R_TESTS = , NOT_CRAN = true, TAR = auto_tar(), ) and always run /path/to/current/R --vanilla CMD check ... Hadley -- Chief Scientist, RStudio http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Trouble building package using R in development
On Wed, 2013-01-16 at 14:39 -0600, Hadley Wickham wrote: To circumvent this, I check using: R --no-init-file CMD check foo_1.0.tar.gz In devtools, we take considerable care to match the R you're running with the R you're checking in, so we also set the following environmental variables: snip / Thanks Henrik Hadley, and always run /path/to/current/R --vanilla CMD check ... To what end is the --vanilla here? Writing R Extensions says that R CMD check (and R CMD build) are invoked via R --vanilla so that would seem redundant, although my experience from several hours working this through today suggests there is a difference between R --vanilla CMD check and R CMD check. G Hadley -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
