[Rd] Building R on Windows 7 -- No rule to make target `etc/GETDESC', needed by `fixetc'.
Hi all, I have been experiencing difficulties building R (be this 2.13.1, beta, devel, or rc) on Windows 7 64bit. I believe I am following the manual religiously, and don't think I am doing anything differently from the many successful build attempts in the past. Unzipping the tarball works fine, but when I invoke make, I get (shown for R-rc, same for 2-13.1): H:\R_Builds\R-rc\src\gnuwin32make all recommended cat MkRules.dist MkRules.rules MkRules Building ../../../library/base/R/Rprofile from ../../library/profile/Common.R ../../library/profile/Rprofile.windows mkdir -p ../../../library/base/R cp -p html/rwin.html ../../../doc/html/index.html make[3]: *** No rule to make target `etc/GETDESC', needed by `fixetc'. Stop. make[2]: *** [fixfiles] Error 2 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 Any help? Thanks, Jo __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Building R on Windows 7 -- No rule to make target `etc/GETDESC', needed by `fixetc'.
Fine for me with R-2.13.2 RC. No idea where you got the differences from. Perhaps reinstall recent version of the Rtools, check the PATH, make sure this is a clean checkout / directory and try again. Uwe ligges On 23.09.2011 13:46, Johannes Egner wrote: Hi all, I have been experiencing difficulties building R (be this 2.13.1, beta, devel, or rc) on Windows 7 64bit. I believe I am following the manual religiously, and don't think I am doing anything differently from the many successful build attempts in the past. Unzipping the tarball works fine, but when I invoke make, I get (shown for R-rc, same for 2-13.1): H:\R_Builds\R-rc\src\gnuwin32make all recommended cat MkRules.dist MkRules.rules MkRules Building ../../../library/base/R/Rprofile from ../../library/profile/Common.R ../../library/profile/Rprofile.windows mkdir -p ../../../library/base/R cp -p html/rwin.html ../../../doc/html/index.html make[3]: *** No rule to make target `etc/GETDESC', needed by `fixetc'. Stop. make[2]: *** [fixfiles] Error 2 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 Any help? Thanks, Jo __ 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
[Rd] Issue with seek() on gzipped connections in R-devel
Dear all, In R-devel (2011-09-23 r57050), I'm running into a serious problem with seek()ing on connections opened with gzfile(). A warning is generated and the file position does not seek to the requested location. It doesn't seem to occur all the time - I tried to create a small example file to illustrate it, but the problem didn't occur. However, it can be seen with a file I use for testing my packages, which is available through the URL https://github.com/jonclayden/tractor/blob/master/tests/data/nifti/maskedb0_lia.nii.gz?raw=true: con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 Warning message: In seek.connection(con, 352) : seek on a gzfile connection returned an internal error seek(con, NA) [1] 190 The same commands with the same file work as expected in R 2.13.1, and have worked over many previous versions of R. con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 seek(con, NA) [1] 352 My sessionInfo() output is: R Under development (unstable) (2011-09-23 r57050) Platform: x86_64-apple-darwin11.1.0 (64-bit) locale: [1] en_GB.UTF-8/en_US.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] tractor.nt_2.0.1 tractor.session_2.0.3 tractor.utils_2.0.0 [4] tractor.base_2.0.3reportr_0.2.0 This seems to occur whether or not R is compiled with --with-system-zlib. I see some zlib-related changes mentioned in the NEWS, but I don't see any indication that this is expected. Could anyone shed any light on it, please? Thanks and all the best, Jon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Issue with seek() on gzipped connections in R-devel
Basically seek with zlib is flaky: we've stumbled on several errors. If it worked for you in the past, count yourself lucky. I'd suggest you avoid relying on it in your packages. On Fri, 23 Sep 2011, Jon Clayden wrote: Dear all, In R-devel (2011-09-23 r57050), I'm running into a serious problem with seek()ing on connections opened with gzfile(). A warning is generated and the file position does not seek to the requested location. It doesn't seem to occur all the time - I tried to create a small example file to illustrate it, but the problem didn't occur. However, it can be seen with a file I use for testing my packages, which is available through the URL https://github.com/jonclayden/tractor/blob/master/tests/data/nifti/maskedb0_lia.nii.gz?raw=true: con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 Warning message: In seek.connection(con, 352) : seek on a gzfile connection returned an internal error seek(con, NA) [1] 190 The same commands with the same file work as expected in R 2.13.1, and have worked over many previous versions of R. con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 seek(con, NA) [1] 352 My sessionInfo() output is: R Under development (unstable) (2011-09-23 r57050) Platform: x86_64-apple-darwin11.1.0 (64-bit) locale: [1] en_GB.UTF-8/en_US.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] tractor.nt_2.0.1 tractor.session_2.0.3 tractor.utils_2.0.0 [4] tractor.base_2.0.3reportr_0.2.0 This seems to occur whether or not R is compiled with --with-system-zlib. I see some zlib-related changes mentioned in the NEWS, but I don't see any indication that this is expected. Could anyone shed any light on it, please? Thanks and all the best, Jon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] should dir(all=TRUE) return . and ..?
dir(all=TRUE) returns the file names . and .. while dir(recursive=TRUE, all=TRUE, include.dirs=TRUE) does not. I always filter out the . and .. entries and was wondering if anyone would mind if dir(all=TRUE) just omitted them? It might make recursive file operations like cleaning out a directory safer, as unlink(recursive=TRUE, dir(all=TRUE, dirToClean)) might start attacking dirToClean/.., then dirToClean/../.., etc., until your disk is empty. dir.create(tdir - tempfile(tdir)) file.create(file.path(tdir, c(.dotFile, noDotFile))) [1] TRUE TRUE dir.create(file.path(tdir, .dotDir)) file.create(file.path(tdir, .dotDir, c(noDotFileInDotDir, .dotFileInDotDir))) [1] TRUE TRUE dir(tdir, all=TRUE) # omit . and .. here? [1] . ...dotDir .dotFile [5] noDotFile dir(tdir, all=TRUE, recursive=TRUE, include.dirs=TRUE) [1] .dotDir .dotDir/.dotFileInDotDir [3] .dotDir/noDotFileInDotDir .dotFile [5] noDotFile Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Issue with seek() on gzipped connections in R-devel
seek() in general is a bad idea IMO if you are writing cross-platform code. ?seek Warning: Use of ‘seek’ on Windows is discouraged. We have found so many errors in the Windows implementation of file positioning that users are advised to use it only at their own risk, and asked not to waste the R developers' time with bug reports on Windows' deficiencies. Aside from making me laugh, the above highlights the core reason to not use IMO. For not zipped files, you can try the mmap package. ?mmap and ?types are good starting points. Allows for accessing binary data on disk with very simple R-like semantics, and is very fast. Not as fast as a sequential read... but fast. At present this is 'little endian' only though, but that describes most of the world today. Best, Jeff On Fri, Sep 23, 2011 at 8:58 AM, Jon Clayden jon.clay...@gmail.com wrote: Dear all, In R-devel (2011-09-23 r57050), I'm running into a serious problem with seek()ing on connections opened with gzfile(). A warning is generated and the file position does not seek to the requested location. It doesn't seem to occur all the time - I tried to create a small example file to illustrate it, but the problem didn't occur. However, it can be seen with a file I use for testing my packages, which is available through the URL https://github.com/jonclayden/tractor/blob/master/tests/data/nifti/maskedb0_lia.nii.gz?raw=true: con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 Warning message: In seek.connection(con, 352) : seek on a gzfile connection returned an internal error seek(con, NA) [1] 190 The same commands with the same file work as expected in R 2.13.1, and have worked over many previous versions of R. con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 seek(con, NA) [1] 352 My sessionInfo() output is: R Under development (unstable) (2011-09-23 r57050) Platform: x86_64-apple-darwin11.1.0 (64-bit) locale: [1] en_GB.UTF-8/en_US.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] tractor.nt_2.0.1 tractor.session_2.0.3 tractor.utils_2.0.0 [4] tractor.base_2.0.3 reportr_0.2.0 This seems to occur whether or not R is compiled with --with-system-zlib. I see some zlib-related changes mentioned in the NEWS, but I don't see any indication that this is expected. Could anyone shed any light on it, please? Thanks and all the best, Jon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com www.esotericR.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Issue with seek() on gzipped connections in R-devel
Thanks for the replies. I take the point, although it does seem like a substantial regression (on non-Windows platforms). I like to keep the external dependencies of my packages minimal, but I will look into the mmap package - thanks, Jeff, for the tip. Aside from that, though, what is the alternative to using seek? If I want to read something at (original, uncompressed) byte offset 352, as here, do I have to read and discard everything that comes before it first? That seems inelegant at best... Regards, Jon On 23 September 2011 16:54, Jeffrey Ryan jeffrey.r...@lemnica.com wrote: seek() in general is a bad idea IMO if you are writing cross-platform code. ?seek Warning: Use of ‘seek’ on Windows is discouraged. We have found so many errors in the Windows implementation of file positioning that users are advised to use it only at their own risk, and asked not to waste the R developers' time with bug reports on Windows' deficiencies. Aside from making me laugh, the above highlights the core reason to not use IMO. For not zipped files, you can try the mmap package. ?mmap and ?types are good starting points. Allows for accessing binary data on disk with very simple R-like semantics, and is very fast. Not as fast as a sequential read... but fast. At present this is 'little endian' only though, but that describes most of the world today. Best, Jeff On Fri, Sep 23, 2011 at 8:58 AM, Jon Clayden jon.clay...@gmail.com wrote: Dear all, In R-devel (2011-09-23 r57050), I'm running into a serious problem with seek()ing on connections opened with gzfile(). A warning is generated and the file position does not seek to the requested location. It doesn't seem to occur all the time - I tried to create a small example file to illustrate it, but the problem didn't occur. However, it can be seen with a file I use for testing my packages, which is available through the URL https://github.com/jonclayden/tractor/blob/master/tests/data/nifti/maskedb0_lia.nii.gz?raw=true: con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 Warning message: In seek.connection(con, 352) : seek on a gzfile connection returned an internal error seek(con, NA) [1] 190 The same commands with the same file work as expected in R 2.13.1, and have worked over many previous versions of R. con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 seek(con, NA) [1] 352 My sessionInfo() output is: R Under development (unstable) (2011-09-23 r57050) Platform: x86_64-apple-darwin11.1.0 (64-bit) locale: [1] en_GB.UTF-8/en_US.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] tractor.nt_2.0.1 tractor.session_2.0.3 tractor.utils_2.0.0 [4] tractor.base_2.0.3 reportr_0.2.0 This seems to occur whether or not R is compiled with --with-system-zlib. I see some zlib-related changes mentioned in the NEWS, but I don't see any indication that this is expected. Could anyone shed any light on it, please? Thanks and all the best, Jon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com www.esotericR.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] could not find function after import
Duncan I have a related question. I need one function from R.utils. But R.utils depends on R.oo and R.methodsS3. so I made R.util an import and then used importFrom() in the namespace. The package passed the check. However when it came to use the function it had not been loaded? do I need to add the upstream packages that R.util depends upon? also in the code do I need a library or require? A bit confused Steve On Mon, Sep 19, 2011 at 5:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote: I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat- vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC - rowMeans - is.data.frame - estfun - estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? If you said that your package Depends on sandwich, you'd probably pass checks, but this is arguably a bug in the sandwich package. The problem is that since you only import sandwich, it never gets attached. So it never attaches its dependency zoo. It should import zoo (or import the functions in zoo that it uses) to work properly the way you are calling it. You can see the same error as follows: 1. Install sandwich, but don't attach it or zoo. 2. Run example(glm) to create the glm object glm.D93. Try to call sandwich::estfun(glm.D93) You'll get the same error as before because is.zoo() will not be loaded. It's also arguably a design flaw in R. For testing sandwich, zoo would generally end up being attached, because the testing of sandwich would attach it. However, examples like the one above are never tested. 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] should dir(all=TRUE) return . and ..?
William Dunlap wdun...@tibco.com on Fri, 23 Sep 2011 15:49:43 + writes: dir(all=TRUE) returns the file names . and .. while dir(recursive=TRUE, all=TRUE, include.dirs=TRUE) does not. I always filter out the . and .. entries and was wondering if anyone would mind if dir(all=TRUE) just omitted them? It might make recursive file operations like cleaning out a directory safer, as unlink(recursive=TRUE, dir(all=TRUE, dirToClean)) might start attacking dirToClean/.., then dirToClean/../.., etc., until your disk is empty. :-) Thank you, Bill. I agree that there is a problem. It seems wrong to me that dir(all.files=TRUE, recursive=TRUE, include.dirs=TRUE) *omits* the (symbolic) directories '.' and '..' when simple dir(all.files=TRUE) includes them. However, from a strict description (of the argument names, and also the help file) I would have expected that both would *include* rather than omit them. But then --the scenario abov, and also more general reasoning -- would rather suggest to follow your proposal. Martin dir.create(tdir - tempfile(tdir)) file.create(file.path(tdir, c(.dotFile, noDotFile))) [1] TRUE TRUE dir.create(file.path(tdir, .dotDir)) file.create(file.path(tdir, .dotDir, c(noDotFileInDotDir, .dotFileInDotDir))) [1] TRUE TRUE dir(tdir, all=TRUE) # omit . and .. here? [1] . .. .dotDir .dotFile [5] noDotFile dir(tdir, all=TRUE, recursive=TRUE, include.dirs=TRUE) [1] .dotDir .dotDir/.dotFileInDotDir [3] .dotDir/noDotFileInDotDir .dotFile [5] noDotFile Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Issue with seek() on gzipped connections in R-devel
On Fri, 23 Sep 2011, Jon Clayden wrote: Thanks for the replies. I take the point, although it does seem like a substantial regression (on non-Windows platforms). I like to keep the external dependencies of my packages minimal, but I will look into the mmap package - thanks, Jeff, for the tip. Aside from that, though, what is the alternative to using seek? If I want to read something at (original, uncompressed) byte offset 352, as here, do I have to read and discard everything that comes before it first? That seems inelegant at best... Or uncompress the file. Regards, Jon On 23 September 2011 16:54, Jeffrey Ryan jeffrey.r...@lemnica.com wrote: seek() in general is a bad idea IMO if you are writing cross-platform code. ?seek Warning: Use of ‘seek’ on Windows is discouraged. We have found so many errors in the Windows implementation of file positioning that users are advised to use it only at their own risk, and asked not to waste the R developers' time with bug reports on Windows' deficiencies. Aside from making me laugh, the above highlights the core reason to not use IMO. For not zipped files, you can try the mmap package. ?mmap and ?types are good starting points. Allows for accessing binary data on disk with very simple R-like semantics, and is very fast. Not as fast as a sequential read... but fast. At present this is 'little endian' only though, but that describes most of the world today. Best, Jeff On Fri, Sep 23, 2011 at 8:58 AM, Jon Clayden jon.clay...@gmail.com wrote: Dear all, In R-devel (2011-09-23 r57050), I'm running into a serious problem with seek()ing on connections opened with gzfile(). A warning is generated and the file position does not seek to the requested location. It doesn't seem to occur all the time - I tried to create a small example file to illustrate it, but the problem didn't occur. However, it can be seen with a file I use for testing my packages, which is available through the URL https://github.com/jonclayden/tractor/blob/master/tests/data/nifti/maskedb0_lia.nii.gz?raw=true: con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 Warning message: In seek.connection(con, 352) : seek on a gzfile connection returned an internal error seek(con, NA) [1] 190 The same commands with the same file work as expected in R 2.13.1, and have worked over many previous versions of R. con - gzfile(~/Downloads/maskedb0_lia.nii.gz,rb) seek(con, 352) [1] 0 seek(con, NA) [1] 352 My sessionInfo() output is: R Under development (unstable) (2011-09-23 r57050) Platform: x86_64-apple-darwin11.1.0 (64-bit) locale: [1] en_GB.UTF-8/en_US.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] tractor.nt_2.0.1 tractor.session_2.0.3 tractor.utils_2.0.0 [4] tractor.base_2.0.3 reportr_0.2.0 This seems to occur whether or not R is compiled with --with-system-zlib. I see some zlib-related changes mentioned in the NEWS, but I don't see any indication that this is expected. Could anyone shed any light on it, please? Thanks and all the best, Jon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan jeffrey.r...@lemnica.com www.lemnica.com www.esotericR.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] should dir(all=TRUE) return . and ..?
On Fri, 23 Sep 2011, Martin Maechler wrote: William Dunlap wdun...@tibco.com on Fri, 23 Sep 2011 15:49:43 + writes: dir(all=TRUE) returns the file names . and .. while dir(recursive=TRUE, all=TRUE, include.dirs=TRUE) does not. I always filter out the . and .. entries and was wondering if anyone would mind if dir(all=TRUE) just omitted them? It might make recursive file operations like cleaning out a directory safer, as unlink(recursive=TRUE, dir(all=TRUE, dirToClean)) might start attacking dirToClean/.., then dirToClean/../.., etc., until your disk is empty. :-) Thank you, Bill. I agree that there is a problem. It seems wrong to me that dir(all.files=TRUE, recursive=TRUE, include.dirs=TRUE) *omits* the (symbolic) directories '.' and '..' when simple dir(all.files=TRUE) includes them. It was intentional. The authors of that part wanted it that way, the original author of list.files (aka dir) wanted this the way it was before include.dirs was added. However, from a strict description (of the argument names, and also the help file) I would have expected that both would *include* rather than omit them. But then --the scenario abov, and also more general reasoning -- would rather suggest to follow your proposal. Someone would need to check for back-compatibility though: list.files() has been around for a long time. There are lots of odder things about list.files(), for example that it lists directories with recursive=FALSE and not with recursive=TRUE. So is a directory a file or not? Martin dir.create(tdir - tempfile(tdir)) file.create(file.path(tdir, c(.dotFile, noDotFile))) [1] TRUE TRUE dir.create(file.path(tdir, .dotDir)) file.create(file.path(tdir, .dotDir, c(noDotFileInDotDir, .dotFileInDotDir))) [1] TRUE TRUE dir(tdir, all=TRUE) # omit . and .. here? [1] . .. .dotDir .dotFile [5] noDotFile dir(tdir, all=TRUE, recursive=TRUE, include.dirs=TRUE) [1] .dotDir .dotDir/.dotFileInDotDir [3] .dotDir/noDotFileInDotDir .dotFile [5] noDotFile Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] broken save(..., compress=xy)
Hi, With current R devel and R 2.13.1: aa=1:5 save(aa, file=aa.rda, compress=xy) Error in identical(compress, gzip) || compress : invalid 'y' type in 'x || y' Thanks! H. sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- 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...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] broken save(..., compress=xy)
Hi, 2011/9/23 Hervé Pagès hpa...@fhcrc.org: Hi, With current R devel and R 2.13.1: aa=1:5 save(aa, file=aa.rda, compress=xy) Error in identical(compress, gzip) || compress : invalid 'y' type in 'x || y' The options for compress are gzip bzip2 or xz (and not xy), at least on my linux system. Are you sure you want xy? Sarah Thanks! H. sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- -- Sarah Goslee http://www.functionaldiversity.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] broken save(..., compress=xy)
On 11-09-23 11:02 AM, Sarah Goslee wrote: Hi, 2011/9/23 Hervé Pagèshpa...@fhcrc.org: Hi, With current R devel and R 2.13.1: aa=1:5 save(aa, file=aa.rda, compress=xy) Error in identical(compress, gzip) || compress : invalid 'y' type in 'x || y' The options for compress are gzip bzip2 or xz (and not xy), at least on my linux system. Are you sure you want xy? Right, I wanted xz, sorry... Maybe error handling could be improved though so a typo in the input doesn't break the code? Thanks, H. Sarah Thanks! H. sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- -- 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...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] could not find function after import
On 23/09/2011 12:57 PM, steven mosher wrote: Duncan I have a related question. I need one function from R.utils. But R.utils depends on R.oo and R.methodsS3. so I made R.util an import and then used importFrom() in the namespace. The package passed the check. However when it came to use the function it had not been loaded? do I need to add the upstream packages that R.util depends upon? also in the code do I need a library or require? Sounds exactly like the situation with sandwich below.The workaround available to you is to Depend on R.utils. The author of R.utils could fix the problem by importing R.oo and R.methodsS3, and the authors of R could fix it by changing the behaviour of how R handles imports. Duncan Murdoch A bit confused Steve On Mon, Sep 19, 2011 at 5:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote: I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat- vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC -rowMeans -is.data.frame - estfun -estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? If you said that your package Depends on sandwich, you'd probably pass checks, but this is arguably a bug in the sandwich package. The problem is that since you only import sandwich, it never gets attached. So it never attaches its dependency zoo. It should import zoo (or import the functions in zoo that it uses) to work properly the way you are calling it. You can see the same error as follows: 1. Install sandwich, but don't attach it or zoo. 2. Run example(glm) to create the glm object glm.D93. Try to call sandwich::estfun(glm.D93) You'll get the same error as before because is.zoo() will not be loaded. It's also arguably a design flaw in R. For testing sandwich, zoo would generally end up being attached, because the testing of sandwich would attach it. However, examples like the one above are never tested. 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] could not find function after import
Thanks duncan. I fixed it by changing to depends and resubmitting my packages. But I changed from depends to imports for a very specific reason. namespace conflicts. There are work arounds for that so its not terminally broken, but IMPORT had the promise of just the elegance I was looking for. Thanks for the explanation. Steve On Fri, Sep 23, 2011 at 11:44 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 23/09/2011 12:57 PM, steven mosher wrote: Duncan I have a related question. I need one function from R.utils. But R.utils depends on R.oo and R.methodsS3. so I made R.util an import and then used importFrom() in the namespace. The package passed the check. However when it came to use the function it had not been loaded? do I need to add the upstream packages that R.util depends upon? also in the code do I need a library or require? Sounds exactly like the situation with sandwich below. The workaround available to you is to Depend on R.utils. The author of R.utils could fix the problem by importing R.oo and R.methodsS3, and the authors of R could fix it by changing the behaviour of how R handles imports. Duncan Murdoch A bit confused Steve On Mon, Sep 19, 2011 at 5:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-09-19 4:48 PM, Stephanie M. Gogarten wrote: I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the sandwich package. I have references to sandwich in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat- vcovHC(mod, type=HC0) I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (2011-08-29 r56828) * using platform: x86_64-apple-darwin9.8.0 (64-bit) ... * checking examples ... ERROR ... Error in estfun.glm(x) : could not find function is.zoo Calls: assocTestRegression ... meatHC - rowMeans - is.data.frame - estfun - estfun.glm I import sandwich, sandwich depends on zoo, but a function in zoo cannot be found during execution. I tried to get around this by explicitly including a require statement in assocTestRegression: require(sandwich) The example now runs, but I have a warning in R CMD check: * checking for unstated dependencies in R code ... WARNING ‘library’ or ‘require’ call not declared from: ‘sandwich’ I am not sure why this is a problem, as there is a require statement (for a different package) in another function which does not cause any warnings. Can anyone advise on how to get my package to successfully pass R CMD check? If you said that your package Depends on sandwich, you'd probably pass checks, but this is arguably a bug in the sandwich package. The problem is that since you only import sandwich, it never gets attached. So it never attaches its dependency zoo. It should import zoo (or import the functions in zoo that it uses) to work properly the way you are calling it. You can see the same error as follows: 1. Install sandwich, but don't attach it or zoo. 2. Run example(glm) to create the glm object glm.D93. Try to call sandwich::estfun(glm.D93) You'll get the same error as before because is.zoo() will not be loaded. It's also arguably a design flaw in R. For testing sandwich, zoo would generally end up being attached, because the testing of sandwich would attach it. However, examples like the one above are never tested. 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
[Rd] cbind() crashes on raw vectors
Hi, cbind() doesn't seem to like raw vectors: df - cbind(a=integer(4000), b=raw(4000)) df *** glibc detected *** /home/hpages/R-2.13.1/bin/exec/R: malloc(): memory corruption: 0x02d73ca0 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x79d7a)[0x7f3592b91d7a] /lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x6e)[0x7f3592b9431e] /lib/libreadline.so.5(xmalloc+0x6)[0x7f3592620ab6] /lib/libreadline.so.5(add_history+0xbe)[0x7f359262136e] /home/hpages/R-2.13.1/lib/libR.so(+0x1b6538)[0x7f35936bd538] /lib/libreadline.so.5(rl_callback_read_char+0x8c)[0x7f359261cb1c] /home/hpages/R-2.13.1/lib/libR.so(+0x1b6f74)[0x7f35936bdf74] /home/hpages/R-2.13.1/lib/libR.so(Rf_ReplIteration+0xe7)[0x7f3593610eb7] /home/hpages/R-2.13.1/lib/libR.so(+0x10a260)[0x7f3593611260] /home/hpages/R-2.13.1/lib/libR.so(run_Rmainloop+0x50)[0x7f3593611780] /home/hpages/R-2.13.1/bin/exec/R(main+0x1b)[0x40085b] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7f3592b36eff] /home/hpages/R-2.13.1/bin/exec/R[0x400779] === Memory map: 0040-00401000 r-xp 08:01 3811201 /home/hpages/R-2.13.1/bin/exec/R 0060-00601000 r--p 08:01 3811201 /home/hpages/R-2.13.1/bin/exec/R 00601000-00602000 rw-p 1000 08:01 3811201 /home/hpages/R-2.13.1/bin/exec/R 02583000-03b16000 rw-p 00:00 0 [heap] 7f358c00-7f358c021000 rw-p 00:00 0 7f358c021000-7f359000 ---p 00:00 0 7f3590342000-7f3590357000 r-xp 08:06 8155 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f3590357000-7f3590556000 ---p 00015000 08:06 8155 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f3590556000-7f3590557000 r--p 00014000 08:06 8155 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f3590557000-7f3590558000 rw-p 00015000 08:06 8155 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f3590558000-7f35905c4000 r-xp 08:01 3818237 /home/hpages/R-2.13.1/library/stats/libs/stats.so 7f35905c4000-7f35907c3000 ---p 0006c000 08:01 3818237 /home/hpages/R-2.13.1/library/stats/libs/stats.so 7f35907c3000-7f35907c5000 r--p 0006b000 08:01 3818237 /home/hpages/R-2.13.1/library/stats/libs/stats.so 7f35907c5000-7f35907c7000 rw-p 0006d000 08:01 3818237 /home/hpages/R-2.13.1/library/stats/libs/stats.so 7f35907c7000-7f359083a000 rw-p 00:00 0 7f359083a000-7f359085c000 r-xp 08:01 3817784 /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so 7f359085c000-7f3590a5b000 ---p 00022000 08:01 3817784 /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so 7f3590a5b000-7f3590a5c000 r--p 00021000 08:01 3817784 /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so 7f3590a5c000-7f3590a5d000 rw-p 00022000 08:01 3817784 /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so 7f3590b61000-7f3590b63000 r-xp 08:07 671027 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f3590b63000-7f3590d62000 ---p 2000 08:07 671027 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f3590d62000-7f3590d63000 r--p 1000 08:07 671027 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f3590d63000-7f3590d64000 rw-p 2000 08:07 671027 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so 7f3590d64000-7f3590de6000 rw-p 00:00 0 7f3590de6000-7f3590ded000 r-xp 08:01 3818288 /home/hpages/R-2.13.1/library/methods/libs/methods.so 7f3590ded000-7f3590fec000 ---p 7000 08:01 3818288 /home/hpages/R-2.13.1/library/methods/libs/methods.so 7f3590fec000-7f3590fed000 r--p 6000 08:01 3818288 /home/hpages/R-2.13.1/library/methods/libs/methods.so 7f3590fed000-7f3590fee000 rw-p 7000 08:01 3818288 /home/hpages/R-2.13.1/library/methods/libs/methods.so 7f3590fee000-7f3590ffa000 r-xp 08:06 8319 /lib/x86_64-linux-gnu/libnss_files-2.13.so 7f3590ffa000-7f35911f9000 ---p c000 08:06 8319 /lib/x86_64-linux-gnu/libnss_files-2.13.so 7f35911f9000-7f35911fa000 r--p b000 08:06 8319 /lib/x86_64-linux-gnu/libnss_files-2.13.so 7f35911fa000-7f35911fb000 rw-p c000 08:06 8319 /lib/x86_64-linux-gnu/libnss_files-2.13.so 7f35911fb000-7f3591206000 r-xp 08:06 8321 /lib/x86_64-linux-gnu/libnss_nis-2.13.so 7f3591206000-7f3591405000 ---p b000 08:06 8321 /lib/x86_64-linux-gnu/libnss_nis-2.13.so 7f3591405000-7f3591406000 r--p a000 08:06 8321 /lib/x86_64-linux-gnu/libnss_nis-2.13.so 7f3591406000-7f3591407000 rw-p b000 08:06 8321 /lib/x86_64-linux-gnu/libnss_nis-2.13.so 7f3591407000-7f359141e000 r-xp 08:06 8316 /lib/x86_64-linux-gnu/libnsl-2.13.so 7f359141e000-7f359161d000 ---p 00017000 08:06 8316 /lib/x86_64-linux-gnu/libnsl-2.13.so 7f359161d000-7f359161e000 r--p 00016000 08:06 8316 /lib/x86_64-linux-gnu/libnsl-2.13.so 7f359161e000-7f359161f000 rw-p 00017000 08:06 8316 /lib/x86_64-linux-gnu/libnsl-2.13.so 7f359161f000-7f3591621000 rw-p 00:00 0 7f3591621000-7f3591629000 r-xp 08:06 8317 /lib/x86_64-linux-gnu/libnss_compat-2.13.so 7f3591629000-7f3591828000 ---p 8000 08:06 8317 /lib/x86_64-linux-gnu/libnss_compat-2.13.so
[Rd] inconsolata font for building vignettes with R-devel
Just to save someone else a few seconds of googling: when you try to R CMD check with recent versions of R-devel and you get * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: File `inconsolata.sty' not found. the Debian/Ubuntu solution is: sudo apt-get install texlive-fonts-extra __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] inconsolata font for building vignettes with R-devel
On 23 September 2011 at 18:03, Ben Bolker wrote: | Just to save someone else a few seconds of googling: when you try to R | CMD check with recent versions of R-devel and you get | | * checking PDF version of manual ... WARNING | LaTeX errors when creating PDF version. | This typically indicates Rd problems. | LaTeX errors found: | ! LaTeX Error: File `inconsolata.sty' not found. | | the Debian/Ubuntu solution is: | | sudo apt-get install texlive-fonts-extra Odd. I just built the R 2.13.2 release candidate this morning. My Build-Depends list is Build-Depends: gcc (= 4:4.1.0), g++ (= 4:4.1.0), gfortran (= 4:4.1.0), libblas-dev, liblapack-dev (= 3.1.1), tcl8.5-dev, tk8.5-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (= 7.2.3), texi2html, texinfo (= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, xdg-utils, zlib1g-dev, libpng12-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff4-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, texinfo, texi2html, openjdk-6-jdk [!arm !hppa !kfreebsd-i386 !kfreebsd-amd64 !hurd-i386 !mips] which has texlive-fonts-recommended but t-f-extra as you suggest. Seems not to have any side effects: edd@max:~$ wc -l src/debian/build-logs/r-base_2.13.2~20110922-1.log 17147 src/debian/build-logs/r-base_2.13.2~20110922-1.log edd@max:~$ So is there a safe fallback or not? Should I install texlive-fonts-extra too when building? Dirk -- New Rcpp master class for R and C++ integration is scheduled for San Francisco (Oct 8), more details / reg.info available at http://www.revolutionanalytics.com/products/training/public/rcpp-master-class.php __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] inconsolata font for building vignettes with R-devel
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/23/2011 06:25 PM, Dirk Eddelbuettel wrote: On 23 September 2011 at 18:03, Ben Bolker wrote: | Just to save someone else a few seconds of googling: when you try to R | CMD check with recent versions of R-devel and you get | | * checking PDF version of manual ... WARNING | LaTeX errors when creating PDF version. | This typically indicates Rd problems. | LaTeX errors found: | ! LaTeX Error: File `inconsolata.sty' not found. | | the Debian/Ubuntu solution is: | | sudo apt-get install texlive-fonts-extra Odd. I just built the R 2.13.2 release candidate this morning. My Build-Depends list is Build-Depends: gcc (= 4:4.1.0), g++ (= 4:4.1.0), gfortran (= 4:4.1.0), libblas-dev, liblapack-dev (= 3.1.1), tcl8.5-dev, tk8.5-dev, bison, groff-base, libncurses5-dev, libreadline-dev, debhelper (= 7.2.3), texi2html, texinfo (= 4.1-2), libbz2-dev, liblzma-dev, libpcre3-dev, xdg-utils, zlib1g-dev, libpng12-dev, libjpeg-dev, libx11-dev, libxt-dev, x11proto-core-dev, libpango1.0-dev, libcairo2-dev, libtiff4-dev, xvfb, xauth, xfonts-base, texlive-base, texlive-latex-base, texlive-generic-recommended, texlive-fonts-recommended, texlive-extra-utils, texlive-latex-recommended, texlive-latex-extra, texinfo, texi2html, openjdk-6-jdk [!arm !hppa !kfreebsd-i386 !kfreebsd-amd64 !hurd-i386 !mips] which has texlive-fonts-recommended but t-f-extra as you suggest. Seems not to have any side effects: edd@max:~$ wc -l src/debian/build-logs/r-base_2.13.2~20110922-1.log 17147 src/debian/build-logs/r-base_2.13.2~20110922-1.log edd@max:~$ So is there a safe fallback or not? Should I install texlive-fonts-extra too when building? Dirk I'm on 10.04 LTS which might have something to do with it ... maybe texlive-latex-recommended is a different/older version with less stuff in it? (Maybe ) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iQEcBAEBAgAGBQJOfQfgAAoJED2whTVMEyK9GB0H/2gy7aaGeogtbwT6xDJEqV2G qDeS8/xDS4gXlXm1mXucLcgVyz9GwpT75YfKdGVJTH5m9EDXyeM13I+SyC87VL37 T/g9rIGo4PyqqqipGKO7MRKd799igr6uv+Ua/mzkyWkNptyHZNVwxSgk35GQD6cp l+F6h0a4L6l11dR+HwjtfyRXC8io+/aRF1WlEmfZjwr5P8/soQTDpawi0SSpWrCa Rh32fHE0X2RKiXevrN0yscSRTD7PR3ZdEcqThiKK/6xxF/HM6AW0CD+xVbxpoAz8 3ftXpKCik7z/23tzbskVjuASvvdYWwFGSQiULFS+xOm/aCLrjt/W2RmWlw4Y2C4= =jpMf -END PGP SIGNATURE- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] broken save(..., compress=xy)
Hervé Pagès hpa...@fhcrc.org
on Fri, 23 Sep 2011 11:44:32 -0700 writes:
On 11-09-23 11:02 AM, Sarah Goslee wrote:
Hi,
2011/9/23 Hervé Pagèshpa...@fhcrc.org:
Hi,
With current R devel and R 2.13.1:
aa=1:5 save(aa, file=aa.rda, compress=xy)
Error in identical(compress, gzip) || compress :
invalid 'y' type in 'x || y'
The options for compress are gzip bzip2 or xz (and
not xy), at least on my linux system. Are you sure you
want xy?
Right, I wanted xz, sorry... Maybe error handling could
be improved though so a typo in the input doesn't break
the code?
well, what every ' break the code ' means,
you are right that a more informative error message makes sense
here (though, the code now is slightly longer).
I've committed such a change {svn rev 57057}.
Martin
Thanks, H.
Sarah
Thanks! H.
sessionInfo()
R version 2.13.1 (2011-07-08) Platform:
x86_64-unknown-linux-gnu (64-bit)
locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3]
LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5]
LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7]
LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C
LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8
LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices
utils datasets methods base
--
--
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...@fhcrc.org Phone: (206) 667-5791 Fax: (206)
667-1319
__
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Re: [Rd] cbind() crashes on raw vectors
On 09/23/2011 01:46 PM, Hervé Pagès wrote:
Hi,
cbind() doesn't seem to like raw vectors:
df - cbind(a=integer(4000), b=raw(4000))
df
*** glibc detected *** /home/hpages/R-2.13.1/bin/exec/R: malloc():
memory corruption: 0x02d73ca0 ***
For what it's worth, under valgrind
R -d valgrind -e df - cbind(a=integer(4000), b=raw(4000))
==19446== Memcheck, a memory error detector
==19446== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
==19446== Using Valgrind-3.5.0 and LibVEX; rerun with -h for copyright info
==19446== Command: /home/mtmorgan/bin/R-devel/bin/exec/R --no-save
--quiet -e df~+~\-~+~cbind(a=integer(4000),~+~b=raw(4000))~+~
==19446==
df - cbind(a=integer(4000), b=raw(4000))
==19446== Invalid write of size 8
==19446==at 0x4E8C488: cbind (bind.c:1318)
==19446==by 0x4E8B910: do_bind (bind.c:1117)
==19446==by 0x4F77460: do_internal (names.c:1229)
==19446==by 0x4F14543: Rf_eval (eval.c:469)
==19446==by 0x4F154EC: Rf_applyClosure (eval.c:838)
==19446==by 0x4F14856: Rf_eval (eval.c:513)
==19446==by 0x4F17F19: do_set (eval.c:1724)
==19446==by 0x4F14543: Rf_eval (eval.c:469)
==19446==by 0x4F5D0A8: Rf_ReplIteration (main.c:255)
==19446==by 0x4F5D295: R_ReplConsole (main.c:304)
==19446==by 0x4F5E8F4: run_Rmainloop (main.c:985)
==19446==by 0x4F5E909: Rf_mainloop (main.c:992)
==19446== Address 0x8253298 is 0 bytes after a block of size 32,040 alloc'd
==19446==at 0x4C26C3A: malloc (in
/usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so)
and at bind.c:1306:1319
if (TYPEOF(u) = INTSXP) {
if (mode = INTSXP) {
for (i = 0; i idx; i++)
INTEGER(result)[n++] = INTEGER(u)[i % k];
}
else {
for (i = 0; i idx; i++)
REAL(result)[n++] = (INTEGER(u)[i % k]) == NA_INTEGER ? NA_REAL :
INTEGER(u)[i % k];
}
}
else {
for (i = 0; i idx; i++)
REAL(result)[n++] = REAL(u)[i % k];
}
we end up writing REAL(result)[n++] = REAL(u)[i % k] even though
(gdb) p TYPEOF(u)
$15 = 24
i.e., RAWSXP
(gdb) p TYPEOF(result)
$16 = 13
i.e., INTSXP
it's because the test TYPEOF(u) = INTSXP fails bind.c:1306.
Martin
sessionInfo()
R Under development (unstable) (2011-09-19 r57030)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
=== Backtrace: =
/lib/x86_64-linux-gnu/libc.so.6(+0x79d7a)[0x7f3592b91d7a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x6e)[0x7f3592b9431e]
/lib/libreadline.so.5(xmalloc+0x6)[0x7f3592620ab6]
/lib/libreadline.so.5(add_history+0xbe)[0x7f359262136e]
/home/hpages/R-2.13.1/lib/libR.so(+0x1b6538)[0x7f35936bd538]
/lib/libreadline.so.5(rl_callback_read_char+0x8c)[0x7f359261cb1c]
/home/hpages/R-2.13.1/lib/libR.so(+0x1b6f74)[0x7f35936bdf74]
/home/hpages/R-2.13.1/lib/libR.so(Rf_ReplIteration+0xe7)[0x7f3593610eb7]
/home/hpages/R-2.13.1/lib/libR.so(+0x10a260)[0x7f3593611260]
/home/hpages/R-2.13.1/lib/libR.so(run_Rmainloop+0x50)[0x7f3593611780]
/home/hpages/R-2.13.1/bin/exec/R(main+0x1b)[0x40085b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7f3592b36eff]
/home/hpages/R-2.13.1/bin/exec/R[0x400779]
=== Memory map:
0040-00401000 r-xp 08:01 3811201
/home/hpages/R-2.13.1/bin/exec/R
0060-00601000 r--p 08:01 3811201
/home/hpages/R-2.13.1/bin/exec/R
00601000-00602000 rw-p 1000 08:01 3811201
/home/hpages/R-2.13.1/bin/exec/R
02583000-03b16000 rw-p 00:00 0 [heap]
7f358c00-7f358c021000 rw-p 00:00 0
7f358c021000-7f359000 ---p 00:00 0
7f3590342000-7f3590357000 r-xp 08:06 8155
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f3590357000-7f3590556000 ---p 00015000 08:06 8155
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f3590556000-7f3590557000 r--p 00014000 08:06 8155
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f3590557000-7f3590558000 rw-p 00015000 08:06 8155
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f3590558000-7f35905c4000 r-xp 08:01 3818237
/home/hpages/R-2.13.1/library/stats/libs/stats.so
7f35905c4000-7f35907c3000 ---p 0006c000 08:01 3818237
/home/hpages/R-2.13.1/library/stats/libs/stats.so
7f35907c3000-7f35907c5000 r--p 0006b000 08:01 3818237
/home/hpages/R-2.13.1/library/stats/libs/stats.so
7f35907c5000-7f35907c7000 rw-p 0006d000 08:01 3818237
/home/hpages/R-2.13.1/library/stats/libs/stats.so
7f35907c7000-7f359083a000 rw-p 00:00 0
7f359083a000-7f359085c000 r-xp 08:01 3817784
Re: [Rd] broken save(..., compress=xy)
Hi Martin,
On 11-09-23 04:12 PM, Martin Maechler wrote:
Hervé Pagèshpa...@fhcrc.org
on Fri, 23 Sep 2011 11:44:32 -0700 writes:
On 11-09-23 11:02 AM, Sarah Goslee wrote:
Hi,
2011/9/23 Hervé Pagèshpa...@fhcrc.org:
Hi,
With current R devel and R 2.13.1:
aa=1:5 save(aa, file=aa.rda, compress=xy)
Error in identical(compress, gzip) || compress :
invalid 'y' type in 'x || y'
The options for compress are gzip bzip2 or xz (and
not xy), at least on my linux system. Are you sure you
want xy?
Right, I wanted xz, sorry... Maybe error handling could
be improved though so a typo in the input doesn't break
the code?
well, what every ' break the code ' means,
break here means that the if statement in charge of examining
user input doesn't execute properly for some invalid input.
you are right that a more informative error message makes sense
here (though, the code now is slightly longer).
I've committed such a change {svn rev 57057}.
Thank you!
H.
Martin
Thanks, H.
Sarah
Thanks! H.
sessionInfo()
R version 2.13.1 (2011-07-08) Platform:
x86_64-unknown-linux-gnu (64-bit)
locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3]
LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5]
LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7]
LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C
LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8
LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices
utils datasets methods base
--
--
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...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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