Re: [R-pkg-devel] Note about No repository set, so cyclic dependency check skipped
On 20 July 2015 at 08:53, Martyn Plummer wrote: | On Mon, 2015-07-20 at 07:36 +0200, Antonio José Saez Castillo wrote: | When checking a package I am getting | | * checking package dependencies ... NOTE | No repository set, so cyclic dependency check skipped | | This is an old source of discussion and I've found a lot of suggestions, | but none of them work for me (.Rprofile and/or Rprofile.site edition and | so). What is more worrying is that I'm also getting this note when I check | in R-devel on win-builder site (win-builder.r-project.org). There is | another similar topic in relation to that ( | http://r.789695.n4.nabble.com/No-repository-set-so-cyclic-dependency-check-skipped-td4684184.html), | but I don't know if it is the same problem. | | How can I avoid this note? | | This is covered in the Writing R Extensions manual (page 32), but if you | tried creating a .Rprofile file and it didn't work then the problem | might be that it is in the wrong place. On my Windows 7 desktop, R opens | in my Documents folder rather than my home directory, so my .Rprofile | folder has to go into Documents. If I recall correctly, setting the environment variable HOME (which is not standard under Window) allows you to control that. Files such as ~/.Rprofile will then be searched in the directory pointed to by the value assigned to HOME. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Note about No repository set, so cyclic dependency check skipped
On Mon, 2015-07-20 at 07:36 +0200, Antonio José Saez Castillo wrote:
When checking a package I am getting
* checking package dependencies ... NOTE
No repository set, so cyclic dependency check skipped
This is an old source of discussion and I've found a lot of suggestions,
but none of them work for me (.Rprofile and/or Rprofile.site edition and
so). What is more worrying is that I'm also getting this note when I check
in R-devel on win-builder site (win-builder.r-project.org). There is
another similar topic in relation to that (
http://r.789695.n4.nabble.com/No-repository-set-so-cyclic-dependency-check-skipped-td4684184.html),
but I don't know if it is the same problem.
How can I avoid this note?
This is covered in the Writing R Extensions manual (page 32), but if you
tried creating a .Rprofile file and it didn't work then the problem
might be that it is in the wrong place. On my Windows 7 desktop, R opens
in my Documents folder rather than my home directory, so my .Rprofile
folder has to go into Documents.
Martyn
*Dr. Antonio José Sáez-Castillo*Department of Statistics and
Operational Research
Escuela Politécnica Superior de Linares
UNIVERSIDAD DE JAÉN
C/ Alfonso X el Sabio, 28
23700 Linares (Jaén)
Teléfono: +34 953 64 85 78
e-mail: ajs...@ujaen.es
https://www.researchgate.net/profile/Antonio_Saez-Castillo
http://twitter.com/ajsaezUJA
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[R-pkg-devel] recreating CRAN Testing environment
I am (hopefully) at the end of a series of back-and-forth submissions of a package to the CRAN upload site. I have done my best to test things by: - using devtools - running R CMD check --as-cran on the command line - checking my package on OSX, win-builder.R and various 32 and 64 bit linux virtual machines at DigitalOcean But I have never managed to recreate all of the notes and warning messages that the CRAN testing comes up with. In an effort to save time and effort on both ends, can anyone advise on what I need to do to generate ALL the warning messages that the CRAN testing will find? -- Jonathan Callahan, PhD Mazama Science 206-708-5028 mazamascience.com [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] recreating CRAN Testing environment
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 15-07-20 01:50 PM, Jonathan Callahan wrote: I am (hopefully) at the end of a series of back-and-forth submissions of a package to the CRAN upload site. I have done my best to test things by: - using devtools - running R CMD check --as-cran on the command line - checking my package on OSX, win-builder.R and various 32 and 64 bit linux virtual machines at DigitalOcean But I have never managed to recreate all of the notes and warning messages that the CRAN testing comes up with. In an effort to save time and effort on both ends, can anyone advise on what I need to do to generate ALL the warning messages that the CRAN testing will find? The most important thing that you haven't explicitly mentioned is to test on the most recent development version of R (check out via Subversion/configure/make/make install from scratch). Can you adjust your DigitalOcean settings accordingly? Ben Bolker -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iQEcBAEBAgAGBQJVrTcSAAoJEOCV5YRblxUHNqUIAKMpuDZ5viQSBlyXpIqjtjEW Na6LhC5O/XcjmmrZHDftXAat2gTrRM0OJAn0cfzSZttdcJKowbMYfJzDWe/5oBCE QRQ0zwxbJY1cFHFyYR6r1zCe4ah4SzoGt+FmBYjtAKefvjm12tfQubhQlxPxZ1kV XFIfYTWHmHWNGlhZuokPE/GtdXK5/4MNF/32HxseNBRzc2SWqP3i6VKPnbN7LFgl xrjXsHQdqU3UaY37D44mInl+qm5y5reRSUi6NO0SrSh2WcVWTnqZ3HsUkFPND5tM NyzrfhtGN2wISsFq1J+dC87ajyeh6D8LTYBiokUnWQFOj8tPi1Zhff0LuTJi7Vc= =gytX -END PGP SIGNATURE- __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] recreating CRAN Testing environment
Even if you don't use Windows, it pays to submit your package to the Winbuilder test of buth R-release and R-devel. The error reports, if any, are often not-OS dependant and will serve as a good gaage as to how the real CRAN will respond. Avi On Mon, Jul 20, 2015 at 1:59 PM, Ben Bolker bbol...@gmail.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 15-07-20 01:50 PM, Jonathan Callahan wrote: I am (hopefully) at the end of a series of back-and-forth submissions of a package to the CRAN upload site. I have done my best to test things by: - using devtools - running R CMD check --as-cran on the command line - checking my package on OSX, win-builder.R and various 32 and 64 bit linux virtual machines at DigitalOcean But I have never managed to recreate all of the notes and warning messages that the CRAN testing comes up with. In an effort to save time and effort on both ends, can anyone advise on what I need to do to generate ALL the warning messages that the CRAN testing will find? The most important thing that you haven't explicitly mentioned is to test on the most recent development version of R (check out via Subversion/configure/make/make install from scratch). Can you adjust your DigitalOcean settings accordingly? Ben Bolker -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iQEcBAEBAgAGBQJVrTcSAAoJEOCV5YRblxUHNqUIAKMpuDZ5viQSBlyXpIqjtjEW Na6LhC5O/XcjmmrZHDftXAat2gTrRM0OJAn0cfzSZttdcJKowbMYfJzDWe/5oBCE QRQ0zwxbJY1cFHFyYR6r1zCe4ah4SzoGt+FmBYjtAKefvjm12tfQubhQlxPxZ1kV XFIfYTWHmHWNGlhZuokPE/GtdXK5/4MNF/32HxseNBRzc2SWqP3i6VKPnbN7LFgl xrjXsHQdqU3UaY37D44mInl+qm5y5reRSUi6NO0SrSh2WcVWTnqZ3HsUkFPND5tM NyzrfhtGN2wISsFq1J+dC87ajyeh6D8LTYBiokUnWQFOj8tPi1Zhff0LuTJi7Vc= =gytX -END PGP SIGNATURE- __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] recreating CRAN Testing environment
On Mon, Jul 20, 2015 at 1:59 PM, Ben Bolker bbol...@gmail.com wrote: [...] The most important thing that you haven't explicitly mentioned is to test on the most recent development version of R (check out via Subversion/configure/make/make install from scratch). Can you adjust your DigitalOcean settings accordingly? If you want an easy way to build and check your package with R-devel, and your package is on GitHub, consider using https://github.com/metacran/r-builder By default it builds and checks your package with R-oldrel, R-release and R-devel, on Travis CI. win-builder.r-project.org is another possibility, somewhat complementary. Disclaimer: r-builder is my project, and I have no financial interests in it. Best, Gabor Ben Bolker [...] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] recreating CRAN Testing environment
Thanks to all so far for excellent suggestions! On Mon, Jul 20, 2015 at 11:18 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: On Mon, Jul 20, 2015 at 1:59 PM, Ben Bolker bbol...@gmail.com wrote: [...] The most important thing that you haven't explicitly mentioned is to test on the most recent development version of R (check out via Subversion/configure/make/make install from scratch). Can you adjust your DigitalOcean settings accordingly? If you want an easy way to build and check your package with R-devel, and your package is on GitHub, consider using https://github.com/metacran/r-builder By default it builds and checks your package with R-oldrel, R-release and R-devel, on Travis CI. win-builder.r-project.org is another possibility, somewhat complementary. Disclaimer: r-builder is my project, and I have no financial interests in it. Best, Gabor Ben Bolker [...] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Jonathan Callahan, PhD Mazama Science 206-708-5028 mazamascience.com [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 20 July 2015 at 18:05, MAURICIO ZAMBRANO BIGIARINI wrote: | Dear list, | | I'm trying to set up the development version of R (R-devel ) for | testing some packages before submitting them to CRAN. I'm using Linux | Mint 17.1 64-bit, which is an Ubuntu-based distro. | | I followed the advice of Dirk on | https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html | | | Everything seems to run fine until .configure: | | R is now configured for x86_64-unknown-linux-gnu | | Source directory: . | Installation directory:/usr/local/lib/R-devel | | C compiler:ccache gcc -std=gnu99 -g -O2 | Fortran 77 compiler: gfortran -g -O2 | | C++ compiler: ccache g++ -g -O2 | C++11 compiler:ccache g++ -std=c++11 -g -O2 | Fortran 90/95 compiler:gfortran -g -O2 | Obj-C compiler: | | Interfaces supported: X11, tcltk | External libraries:readline, BLAS(generic), LAPACK(generic), curl | Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU | Options enabled: shared R library, R profiling | | Capabilities skipped: | Options not enabled: shared BLAS, memory profiling | | Recommended packages: no Looks good but ... | | | However, when running make, I got an error saying: | | /usr/bin/ld: ../appl/dchdc.o: relocation R_X86_64_32 against | `.rodata' can not be used when making a shared object; recompile with | -fPIC | | | I would highly appreciate any advice on how to solve this issue (or | what should I recompile with -fPIC and how). ... naybe your R was built without shared library support? The binaries resulting from my configuration (ie the Debian or Ubuntu packages obtained either from the distro themselves or the CRAN mirrors) have 'pic' set: edd@max:~$ grep -i pic /etc/R/Makeconf CPICFLAGS = -fpic CXXPICFLAGS = -fpic CXX1XPICFLAGS = -fpic DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS) FCPICFLAGS = -fpic FPICFLAGS = -fpic SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) ## We want to ensure libR is picked up from $(R_HOME)/lib ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS) ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS) ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS) ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS) ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS) $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ edd@max:~$ Here /etc/R/Makefonf is just a convenient link to $(R_HOME)/etc/Makeconf. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
= When the pupil is ready, the master arrives. (Zen proverb) = Linux user #454569 -- Linux Mint user On 20 July 2015 at 18:35, Dirk Eddelbuettel e...@debian.org wrote: On 20 July 2015 at 18:05, MAURICIO ZAMBRANO BIGIARINI wrote: | Dear list, | | I'm trying to set up the development version of R (R-devel ) for | testing some packages before submitting them to CRAN. I'm using Linux | Mint 17.1 64-bit, which is an Ubuntu-based distro. | | I followed the advice of Dirk on | https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html | | | Everything seems to run fine until .configure: | | R is now configured for x86_64-unknown-linux-gnu | | Source directory: . | Installation directory:/usr/local/lib/R-devel | | C compiler:ccache gcc -std=gnu99 -g -O2 | Fortran 77 compiler: gfortran -g -O2 | | C++ compiler: ccache g++ -g -O2 | C++11 compiler:ccache g++ -std=c++11 -g -O2 | Fortran 90/95 compiler:gfortran -g -O2 | Obj-C compiler: | | Interfaces supported: X11, tcltk | External libraries:readline, BLAS(generic), LAPACK(generic), curl | Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU | Options enabled: shared R library, R profiling | | Capabilities skipped: | Options not enabled: shared BLAS, memory profiling | | Recommended packages: no Looks good but ... | | | However, when running make, I got an error saying: | | /usr/bin/ld: ../appl/dchdc.o: relocation R_X86_64_32 against | `.rodata' can not be used when making a shared object; recompile with | -fPIC | | | I would highly appreciate any advice on how to solve this issue (or | what should I recompile with -fPIC and how). ... naybe your R was built without shared library support? The binaries resulting from my configuration (ie the Debian or Ubuntu packages obtained either from the distro themselves or the CRAN mirrors) have 'pic' set: edd@max:~$ grep -i pic /etc/R/Makeconf CPICFLAGS = -fpic CXXPICFLAGS = -fpic CXX1XPICFLAGS = -fpic DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS) FCPICFLAGS = -fpic FPICFLAGS = -fpic SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) ## We want to ensure libR is picked up from $(R_HOME)/lib ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS) ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS) ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS) ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS) ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS) $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ edd@max:~$ Here /etc/R/Makefonf is just a convenient link to $(R_HOME)/etc/Makeconf. Dirk Thank you very much Dirk, but I forgot to mention that this is my very first time trying to set up R-devel. In my ~/SVN/R-devel/trunk/Makeconf file I currently don't have the first two lines you mentioned: CPICFLAGS = -fpic CXXPICFLAGS = -fpic and instead of SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) I have DYLIB_LDFLAGS = -shared -fopenmp# $(DYLIBS_LTO) how can I be sure that I I enabled the shared library support ? Mauricio __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 20 July 2015 at 18:56, MAURICIO ZAMBRANO BIGIARINI wrote: | how can I be sure that I I enabled the shared library support ? edd@max:~/svn/r-devel$ ./configure --help | grep enable-R-sh --enable-R-shlibbuild the shared/dynamic library 'libR' [no] edd@max:~/svn/r-devel$ Make sure you set --enable-R-shlib. It is in the script which you linked to in your previous email. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 20 July 2015 at 20:29, peter dalgaard pda...@gmail.com wrote: Oi! Could you guys move to r-devel? This has nothing to do with _package_ development. Thanks for the advice. I was not sure about the list I should have submitted this message, but looking at http://www.r-project.org/mail.html: R-package-devel is to get help about package development in R,... If you are having problems developing a package or passing R CMD check, this is the place to ask! R-devel: This list is intended for questions and discussion about code development in R. ... The list is also for proposals of new functionality for R, and pre-testing of new versions. It is meant particularly for those who maintain an active position in the development of R. and as my original intend was to passing R CMD check--as-cran using the development version of R, I chose r-package-devel. I'll create a shorten version of this message in r-devel (not sure if this is the right way of moving a message from one mailing list to another). Mauricio -Peter D On 21 Jul 2015, at 00:49 , MAURICIO ZAMBRANO BIGIARINI mauricio.zambr...@ufrontera.cl wrote: -- Forwarded message -- From: Dirk Eddelbuettel e...@debian.org Date: 20 July 2015 at 19:21 Subject: Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit To: MAURICIO ZAMBRANO BIGIARINI mauricio.zambr...@ufrontera.cl Cc: Dirk Eddelbuettel e...@debian.org, r-package-devel@r-project.org On 20 July 2015 at 18:56, MAURICIO ZAMBRANO BIGIARINI wrote: | how can I be sure that I I enabled the shared library support ? edd@max:~/svn/r-devel$ ./configure --help | grep enable-R-sh --enable-R-shlibbuild the shared/dynamic library 'libR' [no] edd@max:~/svn/r-devel$ Make sure you set --enable-R-shlib. It is in the script which you linked to in your previous email. I thought I did it already when running configure: ./configure --prefix=/usr/local/lib/R-devel --enable-R-shlib --with-blas --with-lapack --with-readline --without-recommended-packages I just tried to run again your script (mentioned in my previous e-mail) from scratch and I'm still getting an error: R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local/lib/R-devel C compiler:ccache gcc -ggdb -pipe -std=gnu99 -Wall -pedantic Fortran 77 compiler: ccache gfortran -g -O2 C++ compiler: ccache g++ -ggdb -pipe -Wall -pedantic C++11 compiler:ccache g++ -std=c++11 -ggdb -pipe -Wall -pedantic Fortran 90/95 compiler:ccache gfortran -g -O2 Obj-C compiler: Interfaces supported: X11, tcltk External libraries:readline, BLAS(generic), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling Capabilities skipped: Options not enabled: shared BLAS, memory profiling Recommended packages: no make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[1]: Nothing to be done for `front-matter'. make[1]: Nothing to be done for `html-non-svn'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' SVN-REVISION is unchanged make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/m4' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/m4' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/tools' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/tools' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/html' make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/html' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/etc' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/etc' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/share' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/share' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' creating src/scripts/R.fe make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/include' config.status: creating src/include/config.h config.status: src/include/config.h is unchanged Rmath.h is unchanged make[3]: Entering
