Re: [Rd] CRAN, Bioconductor and ctv package dependency questions
> Gabor Grothendieck writes: > 1. Can CRAN packages depend on Bioconductor packages and still pass > R CMD check? That is can Suggests: and Depends: in the DESCRIPTION > file contain Bioconductor packages or only other CRAN packages? > Is there an example? Yes, yes, yes. (E.g., LMGene, limma, ...) The only catch is that in the current setup of daily CRAN package checking, packages with non-CRAN dependencies are checked using fake or no installs. > 2. If a package depends on a Bioconductor package does one just list > the package its dependent on or also all packages that that package > recursively depends on? Is this the same as for CRAN packages that > a package is dependent on? Yes. There is a difference between "CRAN style package repositories", as handled by the base R Package Management system, and the main CRAN repository (which of course happens to be a CRAN style one). > 3. Suppose that the output of package A is typically processed by > package B. Thus strictly speaking no function in A depends on any > function in B; however, the output of A is not very usable without > post processing it by B. Would one list A as being dependent on B > anyways? I think this would fall into a third "dependency" category which we currently do not have. > 4. Are there any considerations in the above cases related to > CRAN Task Views (ctv package)? > http://cran.r-project.org/src/contrib/Views/ You would need to talk to the CRAN Task View (ctv) maintainer :-) > 5. Are the above discussed anywhere? I looked up the Depends and > Suggests field in 1.1 of the R Extensions manual but none of the above > is addressed there. Re 1/2: This is because R-exts tells you what to do and not what not to do. Hth -k __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] CRAN, Bioconductor and ctv package dependency questions
On Thu, 8 Sep 2005 10:41:15 +0200 Kurt Hornik wrote:
> > Gabor Grothendieck writes:
>
> > 1. Can CRAN packages depend on Bioconductor packages and still pass
> > R CMD check? That is can Suggests: and Depends: in the DESCRIPTION
> > file contain Bioconductor packages or only other CRAN packages?
> > Is there an example?
>
> Yes, yes, yes. (E.g., LMGene, limma, ...)
>
> The only catch is that in the current setup of daily CRAN package
> checking, packages with non-CRAN dependencies are checked using fake
> or no installs.
>
> > 2. If a package depends on a Bioconductor package does one just list
> > the package its dependent on or also all packages that that package
> > recursively depends on? Is this the same as for CRAN packages that
> > a package is dependent on?
>
> Yes. There is a difference between "CRAN style package repositories",
> as handled by the base R Package Management system, and the main CRAN
> repository (which of course happens to be a CRAN style one).
>
> > 3. Suppose that the output of package A is typically processed by
> > package B. Thus strictly speaking no function in A depends on any
> > function in B; however, the output of A is not very usable without
> > post processing it by B. Would one list A as being dependent on B
> > anyways?
>
> I think this would fall into a third "dependency" category which we
> currently do not have.
>
> > 4. Are there any considerations in the above cases related to
> > CRAN Task Views (ctv package)?
> > http://cran.r-project.org/src/contrib/Views/
>
> You would need to talk to the CRAN Task View (ctv) maintainer :-)
Yes, there are considerations that I have discusses with several people
including Kurt :-)
We're thinking about a way that CRAN style repositories can know what
their name is (CRAN, BioConductor, etc.) and then we could query whether
the repositories in getOption("repos") include a CRAN or a BioC
repository and then have views that include packages from both CRAN and
BioC and potentially other repositories.
Best,
Z
> > 5. Are the above discussed anywhere? I looked up the Depends and
> > Suggests field in 1.1 of the R Extensions manual but none of the
> > above is addressed there.
>
> Re 1/2: This is because R-exts tells you what to do and not what not
> to do.
>
> Hth
>
> -k
>
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Re: [Rd] CRAN, Bioconductor and ctv package dependency questions
> Achim Zeileis writes:
> On Thu, 8 Sep 2005 10:41:15 +0200 Kurt Hornik wrote:
>> > Gabor Grothendieck writes:
>>
>> > 1. Can CRAN packages depend on Bioconductor packages and still pass
>> > R CMD check? That is can Suggests: and Depends: in the DESCRIPTION
>> > file contain Bioconductor packages or only other CRAN packages?
>> > Is there an example?
>>
>> Yes, yes, yes. (E.g., LMGene, limma, ...)
>>
>> The only catch is that in the current setup of daily CRAN package
>> checking, packages with non-CRAN dependencies are checked using fake
>> or no installs.
>>
>> > 2. If a package depends on a Bioconductor package does one just list
>> > the package its dependent on or also all packages that that package
>> > recursively depends on? Is this the same as for CRAN packages that
>> > a package is dependent on?
>>
>> Yes. There is a difference between "CRAN style package repositories",
>> as handled by the base R Package Management system, and the main CRAN
>> repository (which of course happens to be a CRAN style one).
>>
>> > 3. Suppose that the output of package A is typically processed by
>> > package B. Thus strictly speaking no function in A depends on any
>> > function in B; however, the output of A is not very usable without
>> > post processing it by B. Would one list A as being dependent on B
>> > anyways?
>>
>> I think this would fall into a third "dependency" category which we
>> currently do not have.
>>
>> > 4. Are there any considerations in the above cases related to
>> > CRAN Task Views (ctv package)?
>> > http://cran.r-project.org/src/contrib/Views/
>>
>> You would need to talk to the CRAN Task View (ctv) maintainer :-)
> Yes, there are considerations that I have discusses with several
> people including Kurt :-) We're thinking about a way that CRAN style
> repositories can know what their name is (CRAN, BioConductor, etc.)
> and then we could query whether the repositories in getOption("repos")
> include a CRAN or a BioC repository and then have views that include
> packages from both CRAN and BioC and potentially other repositories.
Ah yes. We want to provide repository-side metadata in the style of
Debian's 'Release' files, and take advantage of them. Which has been on
my TODO pile for quite some time now ... how hard can it be to write a
DCF file containing three or four lines ...
-k
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[Rd] Install packages to non-default lib on Windows
We are trying to setup a Windows server that will allow any of our users to build a binary R package given a source package. The idea is to have a central R installation and allow users to install packages to their own package library for the purposes of binary package building. It seems, however, that write access to $R_HOME is required as part of the install step even when -l is used to specify an alternate package library. here's an example of what we're seeing: C:\rlibdir\hpages>set R_LIBS=c:\rlibdir\hpages C:\rlibdir\hpages>d:\biocbld\R-devel\bin\R CMD INSTALL -l=%R_LIBS% --build Biobase_1.6.7.tar.gz Using auto-selected zip options 'Biobase-ZIPDATA=zip Biobase-HELP=ziponly' -- Making package Biobase adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... ... DLL made installing DLL installing R files save image Loading required package: tools Creating a new generic function for 'ncol' in 'Biobase' installing inst files installing data files installing man source files installing indices cannot create d:/biocbld/R-devel/doc/html/search/index.txt: permission denied make[2]: *** [indices] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-Biobase] Error 2 *** Installation of Biobase failed *** Removing 'c:/rlibdir/hpages/Biobase' Questions: - Is it possible to build a binary package on Windows without write access to the $R_HOME tree? - Is it still the case that a side-effect of building a binary package is having that package be installed? My understanding is that R CMD INSTALL --build is the way to get zips on Windows, but maybe this changed? Thanks, + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Wishlist: write.delim()
Hi,
It would be great if someone would add write.delim() as an
adjunct to write.table(), just as with write.csv().
I store a lot of data in tab-delimited files and can read
it in easily with: read.delim("text.txt", as.is=TRUE)
and would love to be able to write it out as easily when
I create these files.
The obvious setting needed for write.delim() is sep = "\t",
but in addition I would request the setting row.names = FALSE
i.e.
write.delim(x, file) = write.table(x, file, sep = "\t", row.names=FALSE)
Thanks much,
Doug Grove
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Re: [Rd] Install packages to non-default lib on Windows
Seth Falcon wrote: > We are trying to setup a Windows server that will allow any of our > users to build a binary R package given a source package. > > The idea is to have a central R installation and allow users to > install packages to their own package library for the purposes of > binary package building. > > It seems, however, that write access to $R_HOME is required as part of > the install step even when -l is used to specify an alternate package > library. > > here's an example of what we're seeing: > > C:\rlibdir\hpages>set R_LIBS=c:\rlibdir\hpages > > C:\rlibdir\hpages>d:\biocbld\R-devel\bin\R CMD INSTALL -l=%R_LIBS% --build > Biobase_1.6.7.tar.gz > > Using auto-selected zip options 'Biobase-ZIPDATA=zip Biobase-HELP=ziponly' > > -- Making package Biobase > adding build stamp to DESCRIPTION > installing NAMESPACE file and metadata > making DLL ... > ... DLL made > installing DLL > installing R files > save image > Loading required package: tools > Creating a new generic function for 'ncol' in 'Biobase' > > installing inst files > installing data files > installing man source files > installing indices > cannot create d:/biocbld/R-devel/doc/html/search/index.txt: permission denied > make[2]: *** [indices] Error 2 > make[1]: *** [all] Error 2 > make: *** [pkg-Biobase] Error 2 > *** Installation of Biobase failed *** > > Removing 'c:/rlibdir/hpages/Biobase' > > > Questions: > > - Is it possible to build a binary package on Windows without write > access to the $R_HOME tree? > > - Is it still the case that a side-effect of building a binary package > is having that package be installed? My understanding is that R CMD > INSTALL --build is the way to get zips on Windows, but maybe this > changed? There are two ways: R CMD INSTALL --build, and R CMD build --binary. The latter doesn't do an install, so the links in help pages don't get generated properly, but it may do a good enough job for what you need. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Rgui error (PR#8126)
Full_Name: Pairoj Khawsithiwong Version: 2.1.1 OS: Window xp Submission from: (NULL) (134.7.248.137) For Windows xp; R for Wnidows GUI front-end has encountered a problem and needs to close. For Windows Me; Rgui caused an error in USER.EXE. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] C macros and Makevars/package building
Hi We are currently embedding a rather large C++ library in R (BioC), and we want some comments on the portability of how we have approach this. First of, we are not really able to do much about the portability of the basic library, which of course is the main question :) We have an approach which seems to work, I just want a bit of feedback on it The way we integrate it into R is simply by having a subdirectory / src/sdk together with a Makevars file. This file basically looks like PKG_CPPFLAGS+=\ -imacros R_affx_constants.h\ -Isdk/files\ (... + a lot of other -I statements telling CPP to include subdirectories of src/sdk) Then we have a SOURCES.SDK = \ sdk/files/FileIO.cpp \ (... + a lot of other .cpp files) SOURCES.OURS = \ R_affx_cdf.cpp and then finally a OBJS=$(SOURCES.SDK:.cpp=.o) $(SOURCES.OURS:cpp:.o) We seem to need the last statement since it seems that .cpp is not automatically a C++ suffix (but is it done the "right" way for portability?). We need the -imacro statement in order to include some macros from Rconfig.h (big endian checks) which are then translated from the WORDS_BIGENDIAN used in R to the IS_BIG_ENDIAN used in the library. Comments on the portability? Kasper __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C macros and Makevars/package building
Kasper Daniel Hansen <[EMAIL PROTECTED]> writes: > Hi > > We are currently embedding a rather large C++ library in R (BioC), > and we want some comments on the portability of how we have approach > this. > > First of, we are not really able to do much about the portability of > the basic library, which of course is the main question :) We have an > approach which seems to work, I just want a bit of feedback on it > > The way we integrate it into R is simply by having a subdirectory / > src/sdk together with a Makevars file. This file basically looks like > > PKG_CPPFLAGS+=\ >-imacros R_affx_constants.h\ >-Isdk/files\ > (... + a lot of other -I statements telling CPP to include > subdirectories of src/sdk) > > Then we have a > > SOURCES.SDK = \ >sdk/files/FileIO.cpp \ >(... + a lot of other .cpp files) > SOURCES.OURS = \ >R_affx_cdf.cpp > > and then finally a > > OBJS=$(SOURCES.SDK:.cpp=.o) $(SOURCES.OURS:cpp:.o) > > We seem to need the last statement since it seems that .cpp is not > automatically a C++ suffix (but is it done the "right" way for > portability?). Er, I don't think it has to do with .cpp being a known suffix or not. If it wasn't, you would use SUFFIXES and a .cpp.o rule. The last line comes from specifying sources, rather than objects. Traditional make style would be OBJS.SDK = \ sdk/files/FileIO.o \ (... + a lot of other .cpp files) OBJS.OURS = \ R_affx_cdf.o OBJS = $(OBJS.SDK) $(OBJS.OURS) from which the suffix rules would deduce the source files. > We need the -imacro statement in order to include some > macros from Rconfig.h (big endian checks) which are then translated > from the WORDS_BIGENDIAN used in R to the IS_BIG_ENDIAN used in the > library. > > Comments on the portability? > > Kasper > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Install packages to non-default lib on Windows
Duncan Murdoch wrote: > Seth Falcon wrote: > >>We are trying to setup a Windows server that will allow any of our >>users to build a binary R package given a source package. >> >>The idea is to have a central R installation and allow users to >>install packages to their own package library for the purposes of >>binary package building. >> >>It seems, however, that write access to $R_HOME is required as part of >>the install step even when -l is used to specify an alternate package >>library. >> >>here's an example of what we're seeing: >> >>C:\rlibdir\hpages>set R_LIBS=c:\rlibdir\hpages >> >>C:\rlibdir\hpages>d:\biocbld\R-devel\bin\R CMD INSTALL -l=%R_LIBS% --build >>Biobase_1.6.7.tar.gz >> >>Using auto-selected zip options 'Biobase-ZIPDATA=zip Biobase-HELP=ziponly' >> >>-- Making package Biobase >> adding build stamp to DESCRIPTION >> installing NAMESPACE file and metadata >> making DLL ... >> ... DLL made >> installing DLL >> installing R files >> save image >>Loading required package: tools >>Creating a new generic function for 'ncol' in 'Biobase' >> >> installing inst files >> installing data files >> installing man source files >> installing indices >>cannot create d:/biocbld/R-devel/doc/html/search/index.txt: permission denied I was also annoyed about this point a couple of times. But what are possible solutions? - not updating indices at all? - provide a switch such as --no-indices for the R CMD tools? - ...? short time workaround: simply give users write access to the few files that have to write to. Uwe Ligges >>make[2]: *** [indices] Error 2 >>make[1]: *** [all] Error 2 >>make: *** [pkg-Biobase] Error 2 >>*** Installation of Biobase failed *** >> >>Removing 'c:/rlibdir/hpages/Biobase' >> >> >>Questions: >> >>- Is it possible to build a binary package on Windows without write >> access to the $R_HOME tree? >> >>- Is it still the case that a side-effect of building a binary package >> is having that package be installed? My understanding is that R CMD >> INSTALL --build is the way to get zips on Windows, but maybe this >> changed? > > > There are two ways: R CMD INSTALL --build, and R CMD build --binary. > The latter doesn't do an install, so the links in help pages don't get > generated properly, but it may do a good enough job for what you need. > > Duncan Murdoch > > __ > 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] Rgui error (PR#8126)
[EMAIL PROTECTED] wrote: > Full_Name: Pairoj Khawsithiwong > Version: 2.1.1 > OS: Window xp > Submission from: (NULL) (134.7.248.137) > > > For Windows xp; > R for Wnidows GUI front-end has encountered a problem and needs to close. > > For Windows Me; > Rgui caused an error in USER.EXE. > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel Unfortunately, this bug report is completely useless. Please tell us exactly how you managed to produce this crash. Please read the Section "R Bugs" in the R FAQ. Uwe Ligges __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
