Re: [Rd] Unexpected failure when calling new() with unnamed arg and
Hervé Pagès hpa...@fredhutch.org on Tue, 12 May 2015 15:18:42 -0700 writes: Hi, The man page for new() suggests that if 'a' is an object with slots slot1 and slot2 and C is a class that extends the class of 'a', then the 2 following calls should be equivalent: new(C, a, ...) new(C, slot1=a@slot1, slot2=a@slot2, ...) This is generally the case but I just ran into a situation where it's not. In the following example the former fails while the latter works: setClass(A, representation(slot1=numeric, slot2=logical)) setClass(B, contains=A, representation(design=formula)) setClass(C, contains=B) a - new(A, slot1=77, slot2=TRUE) new(C, a, design=x ~ y) # fails new(C, slot1=a@slot1, slot2=a@slot2, design=x ~ y) # works Note that new(B, a, design=x ~ y) works so the 3-level class hierarchy is really needed in order to reproduce. Probably related to this, I also noted that new(B) and/or new(C) return invalid objects: c - new(C) validObject(c) # Error in validObject(c) : # invalid class “C” object: invalid object for slot design # in class C: got class S4, should be or extend class formula is(c@design, formula) # [1] FALSE class(c@design) # [1] S4 Note that 'c' can be fixed: c@design - formula(NULL) validObject(c) # [1] TRUE Maybe something that the default initialize method should take care of? Another singularity that is maybe at the root of all of this is that the formula S4 class is virtual: showClass(formula) # Virtual Class formula [package methods] # # Slots: # # Name: .S3Class # Class: character # # Extends: oldClass so a bare call to new(formula) fails: new(formula) # Error in new(formula) : # trying to generate an object from a virtual class (formula) Shouldn't new(formula) just return an empty S3 formula (like formula(NULL) does), in the same way that new(integer) returns an empty ordinary integer vector? Interesting .. and at least worth following. One problem and historical reason for the current setup seems that the formula S3 class is not from 'base' but 'stats' : R's source, src/library/methods/R/BasicClasses.R, lines 524 ff has the following comment block | .OldClassesPrototypes is a list of S3 classes for which prototype | objects are known reasonable. The classes will reappear in | .OldClassesList, but will have been initialized first in | .InitBasicClasses. NB: the methods package will NOT set up | prototypes for S3 classes except those in package base and for ts | (and would rather not do those either). The package that owns the | S3 class should have code to call setOldClass in its | initialization. So, when John Chambers wrote this, he envisioned that the 'stats' package would do the correct thing for its own classes. OTOH, as history went, the stats package was never allowed to depend on methods. There are many other S3 classes from 'stats' which also end up similarly, being defined via setOldClass() and that itself produces a VIRTUAL class. Also, another part of the (R source) comment above is no longer quite accurate, e.g., data.frame is in .OldClassesPrototypes but not in .OldClassesList ... As I do agree that formula is much more basic than these other classes, I'm currently looking at tweaks to the methods (and stats) code, to get this to work as indeed - you mentioned above - we already allow empty S3 formula objects anyway. ... half an hour later : Indeed, I've been able to use the above information such that new(formula) and new(formula, y ~ x) work. However, your code above now --- with my changes --- would fail : setClass(A, representation(slot1=numeric, slot2=logical)) setClass(B, contains=A, representation(design=formula)) setClass(C, contains=B) Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : B is not eligible to be the data part of another class (must be a basic class or a virtual class with no slots) So, I am not yet committing my changes to R-devel. Hopefully more on this, later today. Martin Maechler, ETH Zurich Thanks, H. sessionInfo() R version 3.2.0 Patched (2015-04-17 r68202) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Ubuntu 14.04.2 LTS -- Hervé Pagès Fred Hutchinson Cancer Research Center [..] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Alternative for wildcard gnu extension in Makevars
On 13-05-15 18:08, Gábor Csárdi wrote: On Wed, May 13, 2015 at 12:05 PM, Jan van der Laan rh...@eoos.dds.nl mailto:rh...@eoos.dds.nl wrote: [...] Too bad. Since it is only a handful of files, I will probably move them directly into the src directory and prefix them. It would have been nice to have been able to keep them separate. If it is a couple of files, then you can also just list them in SOURCES (or even just OBJECTS, with a .o suffix), and leave them where they are. That would be a nice solution, but it is a couple (~10) files in the src/boost_src directory. Directly under the src directory there are much more files, and the names and number of these will frequently change so I don't want to keep maintaining this list. Although I could add the generation of Makevars to my build script. Thanks for the suggestion. Jan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Alternative for wildcard gnu extension in Makevars
While at it: 'Makevars' is an R invention (i.e. documentation of it
is only available through the R docs), correct? /Henrik
On Wed, May 13, 2015 at 10:10 AM, Kevin Ushey kevinus...@gmail.com wrote:
One other solution that's only a little crazy: you could have a R
function within your package that generates the appropriate (portable)
Makevars, and within the package `configure` script call that
function. For example
R --vanilla --slave -e source('R/makevars.R'); makevars()
And that 'makevars()' function could generate portable
'Makevars(.win)' files for your package.
Kevin
On Wed, May 13, 2015 at 9:08 AM, Gábor Csárdi csardi.ga...@gmail.com wrote:
On Wed, May 13, 2015 at 12:05 PM, Jan van der Laan rh...@eoos.dds.nl
wrote:
[...]
Too bad. Since it is only a handful of files, I will probably move them
directly into the src directory and prefix them. It would have been nice to
have been able to keep them separate.
If it is a couple of files, then you can also just list them in SOURCES (or
even just OBJECTS, with a .o suffix), and leave them where they are.
Gabor
[...]
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Re: [Bioc-devel] Use and Usability metrics / shields
- Original Message - From: Martin Morgan mtmor...@fredhutch.org To: bioc-devel@r-project.org Sent: Saturday, May 9, 2015 10:15:13 AM Subject: [Bioc-devel] Use and Usability metrics / shields Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. This has now been implemented. You can see it at e.g. http://bioconductor.org/packages/release/bioc/html/BiocGenerics.html The shields are also available for use externally, for example if you want to display build status on a README in Github. Just pull in the image from: http://bioconductor.org/shields/build/release/bioc/BiocGenerics.svg Note that devel has a different build shield: http://bioconductor.org/shields/build/devel/bioc/BiocGenerics.svg Thanks, Dan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Rd] example fails during R CMD CHECK but works interactively?
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 at line 1035. This is completely reproducible when running devtools::check(args='--as-cran') locally. The part that is confusing is that the calls work perfectly when called interactively. Hadley comments on the 'check' page of his R packages website ( http://r-pkgs.had.co.nz/check.html) regarding test failing following R CMD check: Occasionally you may have a problem where the tests pass when run interactively with devtools::test(), but fail when in R CMD check. This usually indicates that you’ve made a faulty assumption about the testing environment, and it’s often hard to figure it out. Any thoughts on how to troubleshoot this problem? I have no idea what assumption we could have made. Regards, Charles [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] example fails during R CMD CHECK but works interactively?
- Original Message - From: Charles Determan cdeterma...@gmail.com To: r-devel@r-project.org Sent: Wednesday, May 13, 2015 11:31:36 AM Subject: [Rd] example fails during R CMD CHECK but works interactively? 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 at line 1035. This is completely reproducible when running devtools::check(args='--as-cran') locally. The part that is confusing is that the calls work perfectly when called interactively. Hadley comments on the 'check' page of his R packages website ( http://r-pkgs.had.co.nz/check.html) regarding test failing following R CMD check: Occasionally you may have a problem where the tests pass when run interactively with devtools::test(), but fail when in R CMD check. This usually indicates that you’ve made a faulty assumption about the testing environment, and it’s often hard to 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 [[alternative HTML version deleted]] __ 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: [Bioc-devel] Use and Usability metrics / shields
Sweet; you went live with the badges/shields, e.g. http://bioconductor.org/packages/release/bioc/html/affxparser.html A positive side effect is that now there's a link from the package page to to the package's check results, which I always wanted :) Thanks for adding this /Henrik On Sun, May 10, 2015 at 11:39 AM, COMMO Frederic frederic.co...@gustaveroussy.fr wrote: Dear Martin, All of these suggestions sound good. Wolfgang's suggestion regarding possible associated papers might be also great. Another useful information would be to point to other publications where a given package was used, and cited. I don't know if it's technically possible, but it would be greatly informative to know how frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015 19:57 À : Martin Morgan Cc: bioc-devel@r-project.org Objet : Re: [Bioc-devel] Use and Usability metrics / shields Dear Martin great idea. Current build status” could perhaps be wrapped with Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCentral actually useful. (i) could be flawed if package and paper are diverged; (ii) would require good disambiguation, e.g. like bioNerDS http://www.biomedcentral.com/1471-2105/14/194 (or other tools? not my expertise). Do we have someone with capabilities in this area on this list? PS Martin you’ll like Fig. 2 of their paper. Wolfgang On May 9, 2015, at 19:15 GMT+2, Martin Morgan mtmor...@fredhutch.org wrote: Bioc developers! It's important that our users be able to identify packages that are suitable for their research question. Obviously a first step is to identify packages in the appropriate research domain, for instance through biocViews. http://bioconductor.org/packages/release/ We'd like to help users further prioritize their efforts by summarizing use and usability. Metrics include: - Cross-platform availability -- biocLite()-able from all or only some platforms - Support forum activity -- questions and comments / responses, 6 month window - Download percentile -- top 5, 20, 50%, or 'available' - Current build status -- errors or warnings on some or all platforms - Developer activity -- commits in the last 6 months - Historical presence -- years in Bioconductor Obviously the metrics are imperfect, so constructive feedback welcome -- we think the above capture in a more-or-less objective and computable way the major axes influencing use and usability. We initially intend to prominently display 'shields' (small graphical icons) on package landing pages. Thanks in advance for your comments, Martin Morgan Bioconductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] CRAN check for package on Sparc Solaris
Thank you for the kind offer! Unfortunately, the problem is really Sparc Solaris: http://cran.r-project.org/web/checks/check_results_metafor.html On Solaris x86 and all other flavors, it passes without errors. Best, Wolfgang From: Gábor Csárdi [csardi.ga...@gmail.com] Sent: Wednesday, May 13, 2015 9:53 PM To: Viechtbauer Wolfgang (STAT) Cc: r-devel@r-project.org Subject: Re: [Rd] CRAN check for package on Sparc Solaris Hi Wolfgang, I can test your package, please send it to me in private. Btw. I only have an x86 machine, and no sparc, so if your problem is sparc-specific, then my test is probably useless. Gabor On Wed, May 13, 2015 at 3:48 PM, Viechtbauer Wolfgang (STAT) wolfgang.viechtba...@maastrichtuniversity.nl wrote: Dear All, The metafor package currently fails CRAN checks on Sparc Solaris: http://cran.r-project.org/web/checks/check_results_metafor.html The problem is probably due to an unintended (= stupid) use of identical() in a couple tests. I have changed that to more appropriate tests using all.equal(). However, before I resubmit the package to CRAN, I would really like to make sure that the updated package passes all checks also on Sparc Solaris. The issue/question of how to test packages on Sparc Solaris has come up before: https://stat.ethz.ch/pipermail/r-devel/2010-September/058538.html https://stat.ethz.ch/pipermail/r-devel/2011-November/062430.html Unless anything has changed in the meantime, it seems like the help of kind volunteers is still the only option to conduct such tests. So, is there anybody out there with access to a Sparc machine running Solaris willing to run 'R CMD check --as-cran' on the updated tarball? Would be very much appreciated! Best, Wolfgang __ 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] LDFLAGS defined in R_MAKEVARS_USER file is ignored for R CMD SHLIB on Windows
I have tracked this discrepancy down to the use of `SHLIB_LD` rather than `SHLIB_LINK` in share/make/winshlib.mk https://github.com/wch/r-source/blob/7348d71d1cb18e9c4b55950fd57198e8d2abcc8b/share/make/winshlib.mk. This variable has been used in winshlib.mk since svn r47953 https://github.com/wch/r-source/commit/3ebd185c0745bdc7cb8dd185bd7df5ff7f827f18, however the corresponding shlib.mk for linux has always used `SHLIB_LINK` instead. The attached patch updates the variables in winshlib.mk to use `SHLIB_LINK` and makes the behavior consistent across platforms, which fixes my issue. On Mon, May 11, 2015 at 12:28 PM, Jim Hester james.f.hes...@gmail.com wrote: Example input and output to reproduce this can be found at https://gist.github.com/jimhester/b7f05f50794c88e44b17. I tested this attempting to compile the [digest]( http://cran.r-project.org/web/packages/digest/index.html) package, `run.sh` and `run.bat` were both run in the package source directory on Ubuntu 14.01 and Windows 7 respectively. In particular while the `CFLAGS` values were properly passed to the compiler on both Linux and Windows, the `LDFLAGS` value was only passed to the linker on Linux, which caused the subsequent linking errors on Windows. Perhaps this is intended behavior, if so is there a different compiler variable I can use to pass flags to the linker on Windows? Index: share/make/winshlib.mk === --- share/make/winshlib.mk (revision 68364) +++ share/make/winshlib.mk (working copy) @@ -10,13 +10,13 @@ $(SHLIB): $(OBJECTS) @if test z$(OBJECTS) != z; then \ if test -e $(BASE)-win.def; then \ - echo $(SHLIB_LD) -shared $(DLLFLAGS) -o $@ $(BASE)-win.def $(OBJECTS) $(ALL_LIBS); \ - $(SHLIB_LD) -shared $(DLLFLAGS) -o $@ $(BASE)-win.def $(OBJECTS) $(ALL_LIBS); \ + echo $(SHLIB_LINK) -shared $(DLLFLAGS) -o $@ $(BASE)-win.def $(OBJECTS) $(ALL_LIBS); \ + $(SHLIB_LINK) -shared $(DLLFLAGS) -o $@ $(BASE)-win.def $(OBJECTS) $(ALL_LIBS); \ else \ echo EXPORTS tmp.def; \ $(NM) $^ | $(SED) -n $(SYMPAT) $(NM_FILTER) tmp.def; \ - echo $(SHLIB_LD) -shared $(DLLFLAGS) -o $@ tmp.def $(OBJECTS) $(ALL_LIBS); \ - $(SHLIB_LD) -shared $(DLLFLAGS) -o $@ tmp.def $(OBJECTS) $(ALL_LIBS); \ + echo $(SHLIB_LINK) -shared $(DLLFLAGS) -o $@ tmp.def $(OBJECTS) $(ALL_LIBS); \ + $(SHLIB_LINK) -shared $(DLLFLAGS) -o $@ tmp.def $(OBJECTS) $(ALL_LIBS); \ $(RM) tmp.def; \ fi \ fi __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] example fails during R CMD CHECK but works interactively?
Thank you Dan but it isn't my tests that are failing (all of them pass without problem) but one of the examples from the inst/examples directory. I did try, however, to start R with the environmental variables as you suggest but it had no effect on my tests. Charles On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Charles Determan cdeterma...@gmail.com To: r-devel@r-project.org Sent: Wednesday, May 13, 2015 11:31:36 AM Subject: [Rd] example fails during R CMD CHECK but works interactively? 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 at line 1035. This is completely reproducible when running devtools::check(args='--as-cran') locally. The part that is confusing is that the calls work perfectly when called interactively. Hadley comments on the 'check' page of his R packages website ( http://r-pkgs.had.co.nz/check.html) regarding test failing following R CMD check: Occasionally you may have a problem where the tests pass when run interactively with devtools::test(), but fail when in R CMD check. This usually indicates that you’ve made a faulty assumption about the testing environment, and it’s often hard to 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 [[alternative HTML version deleted]] __ 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
Re: [Rd] CRAN check for package on Sparc Solaris
Hi Wolfgang, I can test your package, please send it to me in private. Btw. I only have an x86 machine, and no sparc, so if your problem is sparc-specific, then my test is probably useless. Gabor On Wed, May 13, 2015 at 3:48 PM, Viechtbauer Wolfgang (STAT) wolfgang.viechtba...@maastrichtuniversity.nl wrote: Dear All, The metafor package currently fails CRAN checks on Sparc Solaris: http://cran.r-project.org/web/checks/check_results_metafor.html The problem is probably due to an unintended (= stupid) use of identical() in a couple tests. I have changed that to more appropriate tests using all.equal(). However, before I resubmit the package to CRAN, I would really like to make sure that the updated package passes all checks also on Sparc Solaris. The issue/question of how to test packages on Sparc Solaris has come up before: https://stat.ethz.ch/pipermail/r-devel/2010-September/058538.html https://stat.ethz.ch/pipermail/r-devel/2011-November/062430.html Unless anything has changed in the meantime, it seems like the help of kind volunteers is still the only option to conduct such tests. So, is there anybody out there with access to a Sparc machine running Solaris willing to run 'R CMD check --as-cran' on the updated tarball? Would be very much appreciated! Best, Wolfgang __ 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] CRAN check for package on Sparc Solaris
Dear All, The metafor package currently fails CRAN checks on Sparc Solaris: http://cran.r-project.org/web/checks/check_results_metafor.html The problem is probably due to an unintended (= stupid) use of identical() in a couple tests. I have changed that to more appropriate tests using all.equal(). However, before I resubmit the package to CRAN, I would really like to make sure that the updated package passes all checks also on Sparc Solaris. The issue/question of how to test packages on Sparc Solaris has come up before: https://stat.ethz.ch/pipermail/r-devel/2010-September/058538.html https://stat.ethz.ch/pipermail/r-devel/2011-November/062430.html Unless anything has changed in the meantime, it seems like the help of kind volunteers is still the only option to conduct such tests. So, is there anybody out there with access to a Sparc machine running Solaris willing to run 'R CMD check --as-cran' on the updated tarball? Would be very much appreciated! Best, Wolfgang __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Unexpected failure when calling new() with unnamed arg and
Thanks Martin for looking into this. H. On 05/13/2015 03:57 AM, Martin Maechler wrote: Hervé Pagès hpa...@fredhutch.org on Tue, 12 May 2015 15:18:42 -0700 writes: Hi, The man page for new() suggests that if 'a' is an object with slots slot1 and slot2 and C is a class that extends the class of 'a', then the 2 following calls should be equivalent: new(C, a, ...) new(C, slot1=a@slot1, slot2=a@slot2, ...) This is generally the case but I just ran into a situation where it's not. In the following example the former fails while the latter works: setClass(A, representation(slot1=numeric, slot2=logical)) setClass(B, contains=A, representation(design=formula)) setClass(C, contains=B) a - new(A, slot1=77, slot2=TRUE) new(C, a, design=x ~ y) # fails new(C, slot1=a@slot1, slot2=a@slot2, design=x ~ y) # works Note that new(B, a, design=x ~ y) works so the 3-level class hierarchy is really needed in order to reproduce. Probably related to this, I also noted that new(B) and/or new(C) return invalid objects: c - new(C) validObject(c) # Error in validObject(c) : # invalid class “C” object: invalid object for slot design # in class C: got class S4, should be or extend class formula is(c@design, formula) # [1] FALSE class(c@design) # [1] S4 Note that 'c' can be fixed: c@design - formula(NULL) validObject(c) # [1] TRUE Maybe something that the default initialize method should take care of? Another singularity that is maybe at the root of all of this is that the formula S4 class is virtual: showClass(formula) # Virtual Class formula [package methods] # # Slots: # # Name: .S3Class # Class: character # # Extends: oldClass so a bare call to new(formula) fails: new(formula) # Error in new(formula) : # trying to generate an object from a virtual class (formula) Shouldn't new(formula) just return an empty S3 formula (like formula(NULL) does), in the same way that new(integer) returns an empty ordinary integer vector? Interesting .. and at least worth following. One problem and historical reason for the current setup seems that the formula S3 class is not from 'base' but 'stats' : R's source, src/library/methods/R/BasicClasses.R, lines 524 ff has the following comment block | .OldClassesPrototypes is a list of S3 classes for which prototype | objects are known reasonable. The classes will reappear in | .OldClassesList, but will have been initialized first in | .InitBasicClasses. NB: the methods package will NOT set up | prototypes for S3 classes except those in package base and for ts | (and would rather not do those either). The package that owns the | S3 class should have code to call setOldClass in its | initialization. So, when John Chambers wrote this, he envisioned that the 'stats' package would do the correct thing for its own classes. OTOH, as history went, the stats package was never allowed to depend on methods. There are many other S3 classes from 'stats' which also end up similarly, being defined via setOldClass() and that itself produces a VIRTUAL class. Also, another part of the (R source) comment above is no longer quite accurate, e.g., data.frame is in .OldClassesPrototypes but not in .OldClassesList ... As I do agree that formula is much more basic than these other classes, I'm currently looking at tweaks to the methods (and stats) code, to get this to work as indeed - you mentioned above - we already allow empty S3 formula objects anyway. ... half an hour later : Indeed, I've been able to use the above information such that new(formula) and new(formula, y ~ x) work. However, your code above now --- with my changes --- would fail : setClass(A, representation(slot1=numeric, slot2=logical)) setClass(B, contains=A, representation(design=formula)) setClass(C, contains=B) Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : B is not eligible to be the data part of another class (must be a basic class or a virtual class with no slots) So, I am not yet committing my changes to R-devel. Hopefully more on this, later today. Martin Maechler, ETH Zurich Thanks, H. sessionInfo() R version 3.2.0 Patched (2015-04-17 r68202) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Ubuntu 14.04.2 LTS -- Hervé Pagès Fred Hutchinson Cancer Research Center [..] -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Alternative for wildcard gnu extension in Makevars
I have some cpp-files from another library (boost) in a subdirectory in my src directory (src/boost_src). I include these using the following two lines in my Makevars: SOURCES = $(wildcard *.cpp boost_src/*.cpp) OBJECTS = $(SOURCES:.cpp=.o) However, R CMD check complains about my use of 'wildcard'. How do I handle this without any gnu extensions? Thanks. Jan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Alternative for wildcard gnu extension in Makevars
On 13 May 2015 at 17:27, Jan van der Laan wrote: | | I have some cpp-files from another library (boost) in a subdirectory | in my src directory (src/boost_src). I include these using the | following two lines in my Makevars: | | SOURCES = $(wildcard *.cpp boost_src/*.cpp) | OBJECTS = $(SOURCES:.cpp=.o) | | However, R CMD check complains about my use of 'wildcard'. How do I | handle this without any gnu extensions? I looked into this a few weeks (months?) ago, and it would appear that you cannot. I would recommend the alternative offered in Writing R Extensions: renamed it GNUmakefile or add a SystemRequirements: GNU make. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Alternative for wildcard gnu extension in Makevars
On Wed, May 13, 2015 at 12:05 PM, Jan van der Laan rh...@eoos.dds.nl wrote: [...] Too bad. Since it is only a handful of files, I will probably move them directly into the src directory and prefix them. It would have been nice to have been able to keep them separate. If it is a couple of files, then you can also just list them in SOURCES (or even just OBJECTS, with a .o suffix), and leave them where they are. Gabor [...] [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Alternative for wildcard gnu extension in Makevars
Dirk Eddelbuettel e...@debian.org schreef: On 13 May 2015 at 17:27, Jan van der Laan wrote: | | I have some cpp-files from another library (boost) in a subdirectory | in my src directory (src/boost_src). I include these using the | following two lines in my Makevars: | | SOURCES = $(wildcard *.cpp boost_src/*.cpp) | OBJECTS = $(SOURCES:.cpp=.o) | | However, R CMD check complains about my use of 'wildcard'. How do I | handle this without any gnu extensions? I looked into this a few weeks (months?) ago, and it would appear that you cannot. I would recommend the alternative offered in Writing R Extensions: renamed it GNUmakefile or add a SystemRequirements: GNU make. Too bad. Since it is only a handful of files, I will probably move them directly into the src directory and prefix them. It would have been nice to have been able to keep them separate. Thanks! Jan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Why is the diag function so slow (for extraction)?
As kindly pointed out to me (oh my decaying gray matter), is.object()
is better suited for this test;
$ svn diff src/library/base/R/diag.R
Index: src/library/base/R/diag.R
===
--- src/library/base/R/diag.R (revision 68345)
+++ src/library/base/R/diag.R (working copy)
@@ -23,9 +23,11 @@
stop('nrow' or 'ncol' cannot be specified when 'x' is a matrix)
if((m - min(dim(x))) == 0L) return(vector(typeof(x), 0L))
+nms - dimnames(x)
+nrow - dim(x)[1L]
## NB: need double index to avoid overflows.
-y - c(x)[1 + 0L:(m - 1L) * (dim(x)[1L] + 1)]
-nms - dimnames(x)
+if (is.object(x)) x - c(x)
/Henrik
On Tue, May 12, 2015 at 8:24 PM, Henrik Bengtsson
henrik.bengts...@ucsf.edu wrote:
Along Luke's lines, would(n't) it be enough to look for existence of
attribute 'class' to decide whether to dispatch or not, i.e. if c() is
needed or not? Even without .subset(), there is a remarkable
improvement. I think it's worth condition the code on dispatch or
not. For example:
[HB-X201]{hb}: svn diff diag.R
Index: diag.R
===
--- diag.R (revision 68345)
+++ diag.R (working copy)
@@ -23,9 +23,11 @@
stop('nrow' or 'ncol' cannot be specified when 'x' is a matrix)
if((m - min(dim(x))) == 0L) return(vector(typeof(x), 0L))
+nms - dimnames(x)
+nrow - dim(x)[1L]
## NB: need double index to avoid overflows.
-y - c(x)[1 + 0L:(m - 1L) * (dim(x)[1L] + 1)]
-nms - dimnames(x)
+if (!is.null(attr(x, class))) x - c(x)
+y - x[1 + 0L:(m - 1L) * (nrow + 1)]
if (is.list(nms) !any(sapply(nms, is.null))
identical((nm - nms[[1L]][seq_len(m)]), nms[[2L]][seq_len(m)]))
names(y) - nm
?
/Henrik
On Tue, May 12, 2015 at 5:33 AM, Martin Maechler
maech...@lynne.stat.math.ethz.ch wrote:
Steve Bronder sbron...@stevebronder.com
on Thu, 7 May 2015 11:49:49 -0400 writes:
Is it possible to replace c() with .subset()?
It would be possible, but I think entirely wrong.
.subset() is documented to be an internal function not to be
used lightly and more to the point it is documented to *NOT*
dispatch at all.
If you read and understood what Peter and Luke wrote, you'd not
special case here:
diag() should not work only for pure matrices, but for all
matrix-like objects for which ``the usual methods'' work, such
as
as.vector(.), c(.)
That's why there has been the c(.) in there.
You can always make code faster if you write the code so it only
has to work in one special case .. and work there very fast.
Example below
library(microbenchmark)
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[Rd] Reading exit code of pipe()
Is there a way to get the status code of a pipe() command? The documentation suggests that it might be returned by close, however this does not seem to be the case. con - pipe(cat /etc/passwd, r) stream - readLines(con, n = 10) err - close(con) print(err) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Reading exit code of pipe()
Hi Jeroen, I think `pipe` might just be returning the status code of the underlying command executed; for example, I get a status code of '0' when I test a pipe on `ls`: conn - pipe(ls) stream - readLines(conn) print(close(conn)) Similarly, I get an error code if I try to `ls` a non-existent directory (512 in my case), e.g. conn - pipe(ls /no/path/here/sir) stream - readLines(conn) print(close(conn)) So maybe `cat` just doesn't set a status code, and so there's nothing for R to forward back (ergo -- NULL)? Kevin On Wed, May 13, 2015 at 5:24 PM, Jeroen Ooms jeroen.o...@stat.ucla.edu wrote: Is there a way to get the status code of a pipe() command? The documentation suggests that it might be returned by close, however this does not seem to be the case. con - pipe(cat /etc/passwd, r) stream - readLines(con, n = 10) err - close(con) print(err) __ 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] Alternative for wildcard gnu extension in Makevars
One other solution that's only a little crazy: you could have a R
function within your package that generates the appropriate (portable)
Makevars, and within the package `configure` script call that
function. For example
R --vanilla --slave -e source('R/makevars.R'); makevars()
And that 'makevars()' function could generate portable
'Makevars(.win)' files for your package.
Kevin
On Wed, May 13, 2015 at 9:08 AM, Gábor Csárdi csardi.ga...@gmail.com wrote:
On Wed, May 13, 2015 at 12:05 PM, Jan van der Laan rh...@eoos.dds.nl
wrote:
[...]
Too bad. Since it is only a handful of files, I will probably move them
directly into the src directory and prefix them. It would have been nice to
have been able to keep them separate.
If it is a couple of files, then you can also just list them in SOURCES (or
even just OBJECTS, with a .o suffix), and leave them where they are.
Gabor
[...]
[[alternative HTML version deleted]]
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Re: [Rd] Why is the diag function so slow (for extraction)?
From: Martin Maechler maech...@lynne.stat.math.ethz.ch diag() should not work only for pure matrices, but for all matrix-like objects for which ``the usual methods'' work, such as as.vector(.), c(.) That's why there has been the c(.) in there. You can always make code faster if you write the code so it only has to work in one special case .. and work there very fast. help(diag) gives no hint whatever that diag(x) will work for objects that are matrix-like, but aren't actual matrices. help(c) explicitly says that methods for it are NOT required to convert matrices to vectors. So you're advocating slowing down all ordinary uses of diag to accommodate a usage that nobody thought was important enough to actually document. Radford Neal __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Alternative for wildcard gnu extension in Makevars
On 13 May 2015 at 10:10, Kevin Ushey wrote:
| One other solution that's only a little crazy: you could have a R
| function within your package that generates the appropriate (portable)
| Makevars, and within the package `configure` script call that
| function. For example
|
| R --vanilla --slave -e source('R/makevars.R'); makevars()
|
| And that 'makevars()' function could generate portable
| 'Makevars(.win)' files for your package.
Seconded. I do exactly that in another recent package where I needed another
verboten idiom available only in the widespread and feature-rich GNU make
but not the so-much-more constrained basic make: if statements.
See https://github.com/eddelbuettel/Rblpapi/blob/master/configure where I
need to encode 32 or 64 in the name of shared library. By relying on Rscript
I code around the constraint of not having GNU make. [ That is still a
non-CRAN package but for an unrelated, different reason. ]
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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