Re: [Rd] Build from Source fails on Loading required package Matrix
Uwe: Thanks to your gentle nudge I reread the manual and learned that your preferred version of tar is installed by Rtools. After a little glitch and a July 2 R-help post about a missing file in the tarball, I was able to build the patched version of 2.15.1. The work y'all do is beyond words. In case anyone is interested in the steps I took, here they are: Building R-2.15.1 64-bit from Source on Windows “R_Admin” will refer to the R Installation and Administration manual. Getting the Tools Per Appendix D of R_Admin I downloaded and installed Rtools215.exe from the link at the beginning of that appendix, MiKTeX, and Inno. The installation of RTools automatically set the system version of the PATH variable so that the necessary folders for building R are given in the preferred order. On my machine the RTools were placed in the C:\RTools folder. Per section 3.1.1 of R_Admin, RTools also installed “extra files” in C:\R and C:\R64 –- more below. Getting the Source The 2.15.1 tarball on CRAN’s home has an issue with a missing file (per R-help post on 2012-07-02) so I got the most recent patched version per the instructions of section 1.2 of R_Admin by clicking on last night’s “R-patched…” link at the indicated ftp site. I made a directory in C:\Program Files called R-2.15.1 –- my Windows id has Administrator privileges –- and placed the tarball into that folder. Unpacking I used Rtools' tar to unpack the tarball by opening a command window with Administrator privileges (right click, Run as Administrator), navigating to C:\Program Files\R-2.15.1, and then running tar on the tarball with the “--no-same-owner” option per section 3.1.2 of R_Admin. tar automatically created an R-patched subdirectory within C:\Program Files\R-2.15.1 and placed all the files there. Thus, R_HOME in R_Admin was equivalent to C:\Program Files\R 2.15.1\R patched for this build. Getting the Tools (continued): “the extra files” Per the last two bullets of R_Admin section 3.1.2, I copied the \Tcl subdirectory from C:\R64 (because I’m building the 64-bit version) to C:\Program Files\R-2.15.1\R-patched and copied the three folders in C:\R64\src\gnuwin32\bitmap to the directory C:\Program Files\R-2.15.1\R-patched\src\gnuwin32\bitmap. MkRules.local Per R_Admin 3.1.3, I made a copy of MkRules.dist and made the following changes MkRules.dist MkRules.local MULTI = MULTI = 64 # JPEGDIR JPEGDIR # PNGDIR PNGDIR # TIFFDIR TIFFDIR Building the core files My C:\Temp directory can be written to by almost everyone, so, per section 3.1.3, in the still open command window I set the TMPDIR variable to that folder by SET TMPDIR=C:\Temp. Then “make all recommended” ran without error. C:\Program Files\R-2.15.1\R-patched\bin\x64\Rgui.exe worked. Thanks again! Dan On Wed, Aug 15, 2012 at 9:06 AM, Uwe Ligges wrote: > > > On 15.08.2012 17:53, Dan Murphy wrote: >> >> On Wed, Aug 15, 2012 at 8:04 AM, Simon Urbanek >> wrote: >>> >>> >>> Dan, >>> >>> On Aug 15, 2012, at 10:54 AM, Dan Murphy wrote: >>> Hello: I am building R 2.15.1 from source on a Windows 7 machine with the x64 toolset, MixTeX, and InnoSetup per http://cran.r-project.org/bin/windows/Rtools/. I obtained the source for 2.15.1 via svn from https://svn.r-project.org/R/branches/R-2-15-branch/. >>> >>> >>> Did you also rsync the recommended packages? They are not in the SVN. If >>> in doubt, use released source tar balls. >>> >>> Cheers, >>> Simon >>> >> Thanks, Simon. I should have mentioned that as well. Yes, I did "make >> rsync-recommended" per Chapter 3 of the manual and that worked without >> error. >> >> I first inadvertently had tried to build the 2.16 version in /trunk >> and got that "undefined exports" error, then switched to the >> /R-2-15-branch when I realized /trunk held the development version. >> >> In between the two svn checkouts, I had tried the source tar ball at >> the link R-2.15.1.tar.gz. That terminated much sooner in the build, >> which I thought could have resulted from me using 7-Zip on the tar >> ball (lacking a windows version of your tar), so I went back to the >> subversion checkout method. > > > Please read the R Installation and Administration manual that explains how > to set up your environment under Windows to build R yourself and what tools > are needed. Note that a binary is available from CRAN. > > Uwe Ligges > > > >> >>> >>> This is my first try building R from source. The build seems to go far, then terminates with "undefined exports: .M.classEnv" from the Matrix package, I believe. Here are the last few lines of the build session Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' ** help *** installing help indices ** building package indices Loading required package: Matrix Error in namespaceExpo
Re: [Rd] chown, chgrp?
On 15/08/2012 18:38, peter dalgaard wrote:
On Aug 15, 2012, at 17:56 , Barry Rowlingson wrote:
On Wed, Aug 15, 2012 at 2:47 PM, Simon Urbanek
wrote:
... and moreover with the increasing adoption of ACL on unix and non-existence
of uid/gid on Windows this is more an archaic curiosity so I don't think it
makes sense to add it at this point.
It does however raise the question, "What is Hadley up to now?" :)
Aiming for the fortune file again, Barry?
Anyways, since it is not portable anyway, what was ever wrong with
system(sprintf("chown %s %s", foo, bar)
?
Yes, that is the point. I added Sys.chmod because R's own scripts needed
something portable (both to Windows, and later in the handling of umask
where POSIX allows some wiggle room). We've never needed chown/chgrp.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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[Rd] Compressing data for package builds
Hi, I have two .rda files that I need to include in a package. I've placed them both in a data directory after save() the are around 150Kb each. When I try to check the package I get the following warning Warning: large data file(s) saved inefficiently: size ASCII compress zagoskin.rda 137Kb FALSE none Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress modpoll.rda 124Kb 78Kb xz zagoskin.rda137Kb 6Kbbzip2 Both of these files modpoll.rda and zagoskin.rda have already been compressed from megabytes down to Kb. Also,, the instructions"R CMD build --resave-data" doesnt do anything that I can see so I must be using it wrong. Is there a piece of the puzzle I am missing or instructions better than these: I tried LazyDataCompression and my data.rdb is 90Kb. "Package *tools* has a couple of functions to help with data images: checkRdaFiles reports on the way the image was saved, and resaveRdaFiles will re-save with a different type of compression, including choosing the best type for that particular image. Some packages using LazyData will benefit from using a form of compression other than gzip in the installed lazy-loading database. This can be selected by the --data-compress option to R CMD INSTALL or by using the LazyDataCompression field in the DESCRIPTION file. Useful values are bzip2, xz and the default, gzip. The only way to discover which is best is to try them all and look at the size of the pkgname/data/Rdata.rdb file." [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compressing data for package builds
On Aug 16, 2012, at 5:08 PM, steven mosher wrote: > Hi, > > I have two .rda files that I need to include in a package. I've placed > them both in a data directory > after save() the are around 150Kb each. > > When I try to check the package I get the following warning > > Warning: large data file(s) saved inefficiently: >size ASCII compress > zagoskin.rda 137Kb FALSE none > > Note: significantly better compression could be obtained >by using R CMD build --resave-data > old_size new_size compress > modpoll.rda 124Kb 78Kb xz > zagoskin.rda137Kb 6Kbbzip2 > > Both of these files modpoll.rda and zagoskin.rda have already been > compressed from megabytes down to Kb. > > Also,, the instructions"R CMD build --resave-data" doesnt do anything > that I can see so I must be using it wrong. R CMD build is how you preferably should be creating your package tar ball, so you simply add the --resave-data argument to your already existing R CMD build call which creates the tar ball from your source directory. So can you elaborate on "doesn't do anything I can see"? In what sense? No output? No compression? Cheers, Simon > Is there a piece of the puzzle I am missing or instructions better than > these: I tried LazyDataCompression and my > data.rdb is 90Kb. > > "Package *tools* has a couple of functions to help with data images: > checkRdaFiles reports on the way the image was saved, and resaveRdaFiles will > re-save with a different type of compression, including choosing the best > type for that particular image. > > Some packages using ŒLazyData‚ will benefit from using a form of > compression other than gzip in the installed lazy-loading database. This > can be selected by the --data-compress option to R CMD INSTALL or by using > the ŒLazyDataCompression‚ field in the DESCRIPTION file. Useful values are > bzip2, xz and the default, gzip. The only way to discover which is best is > to try them all and look at the size of the pkgname/data/Rdata.rdb file." > > [[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: [Rd] Compressing data for package builds
" R CMD build is how you preferably should be creating your package tar ball, so you simply add the --resave-data argument to your already existing R CMD build call which creates the tar ball from your source directory. So can you elaborate on "doesn't do anything I can see"? In what sense? No output? No compression? " my tarball builds with > R CDM build mattools where mattools is the name of the package. and I get a warning on R CMD check. Things I tried R CMD build --resave-data R CMD build mattools --resave-data R CMD build --resave-data mattools The first does nothing, the second fails on unknown options and the third fails on unknown options. So I found the help for R CMD Now that I figured out how to display help for R CMD build I see that --resave-data must include a specification of the type of compression --resave-data="best" for example I ran that. and got the same error indicating that the rda file had not been compressed. checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... WARNING Warning: large data file(s) saved inefficiently: size ASCII compress zagoskin.rda 137Kb FALSE none Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress modpoll.rda 124Kb 78Kb xz zagoskin.rda137Kb 6Kbbzip2 Building under windows so I wonder if I am missing a system file required to do the compression. On Thu, Aug 16, 2012 at 5:48 PM, Simon Urbanek wrote: > > On Aug 16, 2012, at 5:08 PM, steven mosher wrote: > > > Hi, > > > > I have two .rda files that I need to include in a package. I've placed > > them both in a data directory > > after save() the are around 150Kb each. > > > > When I try to check the package I get the following warning > > > > Warning: large data file(s) saved inefficiently: > >size ASCII compress > > zagoskin.rda 137Kb FALSE none > > > > Note: significantly better compression could be obtained > >by using R CMD build --resave-data > > old_size new_size compress > > modpoll.rda 124Kb 78Kb xz > > zagoskin.rda137Kb 6Kbbzip2 > > > > Both of these files modpoll.rda and zagoskin.rda have already been > > compressed from megabytes down to Kb. > > > > Also,, the instructions"R CMD build --resave-data" doesnt do > anything > > that I can see so I must be using it wrong. > > R CMD build is how you preferably should be creating your package tar > ball, so you simply add the --resave-data argument to your already existing > R CMD build call which creates the tar ball from your source directory. So > can you elaborate on "doesn't do anything I can see"? In what sense? No > output? No compression? > > Cheers, > Simon > > > > Is there a piece of the puzzle I am missing or instructions better than > > these: I tried LazyDataCompression and my > > data.rdb is 90Kb. > > > > "Package *tools* has a couple of functions to help with data images: > > checkRdaFiles reports on the way the image was saved, and resaveRdaFiles > will > > re-save with a different type of compression, including choosing the best > > type for that particular image. > > > > Some packages using LazyData will benefit from using a form of > > compression other than gzip in the installed lazy-loading database. This > > can be selected by the --data-compress option to R CMD INSTALL or by > using > > the LazyDataCompression field in the DESCRIPTION file. Useful values > are > > bzip2, xz and the default, gzip. The only way to discover which is best > is > > to try them all and look at the size of the pkgname/data/Rdata.rdb file." > > > > [[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
