Re: [Rd] update.packages fails with directory not found
I posted a similar problem to this list but had no response. The full email is copied below. In a nutshell, I traced the message to normalizePath, which issues it. The directory does not exist because a move/rename directory command, issued at the end of the installation, failed. The directory you see would have been renamed to the eventual one otherwise. Since it is the move/rename command which fails on otherwise (seemingly) successful installation, is it possible to try to copy the directory when renaming fails and, if successful, inform the user that a temporary directory has been left behind? Georgi Boshnakov Univeristy of Manchester -- Message: 1 Date: Mon, 10 May 2010 00:07:50 -0400 From: Mike Prager mike.pra...@mhprager.com To: r-de...@stat.math.ethz.ch Subject: [Rd] update.packages fails with directory not found Message-ID: t81fu5t8gg8crt5nm3h3d3rg6bcg7lr...@4ax.com Content-Type: text/plain; charset=us-ascii Windows XP. I have just updated to R 2.11.0 and then run update.packages. In the series of updates, a few will succeed, then I get a failure like package 'mvtnorm' successfully unpacked and MD5 sums checked package 'party' successfully unpacked and MD5 sums checked package 'PBSmodelling' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=c:\Program Files\R\Library/PBSmodelling: The system cannot find the file specified Indeed, the path is missing, though it was there when I issued the update.packages command. ??? -- Mike Prager, NC, USA -- - Forwarded message from georgi.boshna...@manchester.ac.uk - Date: Thu, 18 Feb 2010 10:43:11 + From: Georgi Boshnakov georgi.boshna...@manchester.ac.uk Subject: install.packages, normalizePath, file permissions To: r-devel@r-project.org Dear developers, I have a small but more or less well defined inquiry. Another, more general one for which I was not able to find information is towards the end of this messages. The question seems to be too technical for R-help, that is why I post it here. When installing packages (Windows XP), occasionally the installation does not complete because, it seems, Windows locks some files. I normally ignore this as a minor annoyance but now I wish to ask students to install a number of often used packages by sourcing an R file and this becomes a problem. Here is an example: install.packages( file.path(fp,fgui_1.0-0.zip ), repos=NULL) Warning in install.packages(file.path(fp, fgui_1.0-0.zip), repos = NULL) : argument 'lib' is missing: using 'p:/Rpack' package 'fgui' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=p:\Rpack/fgui: The system cannot find the file specified The circumstances are difficult to reproduce. For some reason, the system does not like fgui and maybe other packages. The p: drive above is network attached and and I have read/write access. Here is the result of traceback. traceback() 7: normalizePath(instPath) 6: sprintf(gettext(fmt, domain = domain), ...) 5: gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)) 4: warning(gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)), domain = NA, call. = FALSE, immediate. = TRUE) 3: unpackPkg(pkgs[i], pkgnames[i], lib) 2: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, dependencies = dependencies, ...) 1: install.packages(file.path(fp, fgui_1.0-0.zip), repos = NULL) The error seems to be thrown by the folloing chunk towards the end of .install.winbinary(): ret - file.rename(file.path(tmpDir, curPkg), instPath) if(!ret) warning(gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)), domain = NA, call. = FALSE, immediate. = TRUE) ... Apparently, renaming failed and a message is displayed. The failure of rename.file may have left the directory specified by 'instPath' non-existent which may cause normalizePath to fail. When this happens the message printed is not that of warninig() but the one from normalizePath() which is uninformative for the user. Maybe an additional check here would be appropriate and, given that the installation has been basically successful at this point, even an attempt to copy the directory after the refusal by Windows to rename it? I understand of course that the developers have better things to do than to wrestle with the caprice of Windows. Here is a more general enquiry. I am using R in a statistics course (about 100) students in a computer cluster where R
Re: [Rd] update.packages fails with directory not found
On 11/05/2010 6:35 AM, Georgi Boshnakov wrote: I posted a similar problem to this list but had no response. The full email is copied below. Thanks for reposting this. I didn't see the original (I was travelling at the time). In a nutshell, I traced the message to normalizePath, which issues it. The directory does not exist because a move/rename directory command, issued at the end of the installation, failed. The directory you see would have been renamed to the eventual one otherwise. I'll change normalizePath to generate a warning rather than an error. This may allow processing to continue. Since it is the move/rename command which fails on otherwise (seemingly) successful installation, is it possible to try to copy the directory when renaming fails and, if successful, inform the user that a temporary directory has been left behind? It was just a warning message about not moving the directory. But the warning message itself triggered an error, which stopped the install. So maybe things will be okay if we just stop the error. The big problem with this particular bug is that it is not reproducible on demand. So I can make changes, but I have no idea if they are effective. Duncan Murdoch Georgi Boshnakov Univeristy of Manchester -- Message: 1 Date: Mon, 10 May 2010 00:07:50 -0400 From: Mike Prager mike.pra...@mhprager.com To: r-de...@stat.math.ethz.ch Subject: [Rd] update.packages fails with directory not found Message-ID: t81fu5t8gg8crt5nm3h3d3rg6bcg7lr...@4ax.com Content-Type: text/plain; charset=us-ascii Windows XP. I have just updated to R 2.11.0 and then run update.packages. In the series of updates, a few will succeed, then I get a failure like package 'mvtnorm' successfully unpacked and MD5 sums checked package 'party' successfully unpacked and MD5 sums checked package 'PBSmodelling' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=c:\Program Files\R\Library/PBSmodelling: The system cannot find the file specified Indeed, the path is missing, though it was there when I issued the update.packages command. ??? -- Mike Prager, NC, USA -- - Forwarded message from georgi.boshna...@manchester.ac.uk - Date: Thu, 18 Feb 2010 10:43:11 + From: Georgi Boshnakov georgi.boshna...@manchester.ac.uk Subject: install.packages, normalizePath, file permissions To: r-devel@r-project.org Dear developers, I have a small but more or less well defined inquiry. Another, more general one for which I was not able to find information is towards the end of this messages. The question seems to be too technical for R-help, that is why I post it here. When installing packages (Windows XP), occasionally the installation does not complete because, it seems, Windows locks some files. I normally ignore this as a minor annoyance but now I wish to ask students to install a number of often used packages by sourcing an R file and this becomes a problem. Here is an example: install.packages( file.path(fp,fgui_1.0-0.zip ), repos=NULL) Warning in install.packages(file.path(fp, fgui_1.0-0.zip), repos = NULL) : argument 'lib' is missing: using 'p:/Rpack' package 'fgui' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=p:\Rpack/fgui: The system cannot find the file specified The circumstances are difficult to reproduce. For some reason, the system does not like fgui and maybe other packages. The p: drive above is network attached and and I have read/write access. Here is the result of traceback. traceback() 7: normalizePath(instPath) 6: sprintf(gettext(fmt, domain = domain), ...) 5: gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)) 4: warning(gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)), domain = NA, call. = FALSE, immediate. = TRUE) 3: unpackPkg(pkgs[i], pkgnames[i], lib) 2: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, dependencies = dependencies, ...) 1: install.packages(file.path(fp, fgui_1.0-0.zip), repos = NULL) The error seems to be thrown by the folloing chunk towards the end of .install.winbinary(): ret - file.rename(file.path(tmpDir, curPkg), instPath) if(!ret) warning(gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)), domain = NA, call. = FALSE, immediate. = TRUE) ... Apparently, renaming failed and a message is displayed. The failure of rename.file may have left the directory specified by
Re: [Rd] update.packages fails with directory not found
On May 11, 2010, at 12:35 PM, Georgi Boshnakov wrote: I posted a similar problem to this list but had no response. The full email is copied below. Well, things sometimes just fly by In a nutshell, I traced the message to normalizePath, which issues it. The directory does not exist because a move/rename directory command, issued at the end of the installation, failed. The directory you see would have been renamed to the eventual one otherwise. Since it is the move/rename command which fails on otherwise (seemingly) successful installation, is it possible to try to copy the directory when renaming fails and, if successful, inform the user that a temporary directory has been left behind? Looks like there is a fundamental issue to solve first, anyway: [...much snippage...] ret - file.rename(file.path(tmpDir, curPkg), instPath) if(!ret) warning(gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)), domain = NA, call. = FALSE, immediate. = TRUE) ... Yes, as your analysis below more or less indicates: There is a logical problem here! If we can only normalize paths to existing files, then we can not use normalizePath in warning messages saying that we couldn't create them. The internal issue would seem to be that do_normalizepath internally calls and checks for success of GetLongPathName or its -W version, and I expect that cannot work on paths that don't exist. Apparently, renaming failed and a message is displayed. The failure of rename.file may have left the directory specified by 'instPath' non-existent which may cause normalizePath to fail. When this happens the message printed is not that of warninig() but the one from normalizePath() which is uninformative for the user. Maybe an additional check here would be appropriate and, given that the installation has been basically successful at this point, even an attempt to copy the directory after the refusal by Windows to rename it? I understand of course that the developers have better things to do than to wrestle with the caprice of Windows. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages fails with directory not found
I've now also committed a change to the file.rename code (on Windows) so that it waits for the file copy to complete before returning. It seems possible that it was returning too early, so the next step of the install failed. I'd appreciate it if you could check whether the problems remain in R-devel, revision 51980 or later. (A build of this revision should be on CRAN by tomorrow, at http://cran.r-project.org/bin/windows/base/rdevel.html .) Duncan Murdoch On 11/05/2010 7:47 AM, Duncan Murdoch wrote: On 11/05/2010 6:35 AM, Georgi Boshnakov wrote: I posted a similar problem to this list but had no response. The full email is copied below. Thanks for reposting this. I didn't see the original (I was travelling at the time). In a nutshell, I traced the message to normalizePath, which issues it. The directory does not exist because a move/rename directory command, issued at the end of the installation, failed. The directory you see would have been renamed to the eventual one otherwise. I'll change normalizePath to generate a warning rather than an error. This may allow processing to continue. Since it is the move/rename command which fails on otherwise (seemingly) successful installation, is it possible to try to copy the directory when renaming fails and, if successful, inform the user that a temporary directory has been left behind? It was just a warning message about not moving the directory. But the warning message itself triggered an error, which stopped the install. So maybe things will be okay if we just stop the error. The big problem with this particular bug is that it is not reproducible on demand. So I can make changes, but I have no idea if they are effective. Duncan Murdoch Georgi Boshnakov Univeristy of Manchester -- Message: 1 Date: Mon, 10 May 2010 00:07:50 -0400 From: Mike Prager mike.pra...@mhprager.com To: r-de...@stat.math.ethz.ch Subject: [Rd] update.packages fails with directory not found Message-ID: t81fu5t8gg8crt5nm3h3d3rg6bcg7lr...@4ax.com Content-Type: text/plain; charset=us-ascii Windows XP. I have just updated to R 2.11.0 and then run update.packages. In the series of updates, a few will succeed, then I get a failure like package 'mvtnorm' successfully unpacked and MD5 sums checked package 'party' successfully unpacked and MD5 sums checked package 'PBSmodelling' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=c:\Program Files\R\Library/PBSmodelling: The system cannot find the file specified Indeed, the path is missing, though it was there when I issued the update.packages command. ??? -- Mike Prager, NC, USA -- - Forwarded message from georgi.boshna...@manchester.ac.uk - Date: Thu, 18 Feb 2010 10:43:11 + From: Georgi Boshnakov georgi.boshna...@manchester.ac.uk Subject: install.packages, normalizePath, file permissions To: r-devel@r-project.org Dear developers, I have a small but more or less well defined inquiry. Another, more general one for which I was not able to find information is towards the end of this messages. The question seems to be too technical for R-help, that is why I post it here. When installing packages (Windows XP), occasionally the installation does not complete because, it seems, Windows locks some files. I normally ignore this as a minor annoyance but now I wish to ask students to install a number of often used packages by sourcing an R file and this becomes a problem. Here is an example: install.packages( file.path(fp,fgui_1.0-0.zip ), repos=NULL) Warning in install.packages(file.path(fp, fgui_1.0-0.zip), repos = NULL) : argument 'lib' is missing: using 'p:/Rpack' package 'fgui' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=p:\Rpack/fgui: The system cannot find the file specified The circumstances are difficult to reproduce. For some reason, the system does not like fgui and maybe other packages. The p: drive above is network attached and and I have read/write access. Here is the result of traceback. traceback() 7: normalizePath(instPath) 6: sprintf(gettext(fmt, domain = domain), ...) 5: gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)) 4: warning(gettextf(unable to move temporary installation '%s' to '%s', normalizePath(file.path(tmpDir, curPkg)), normalizePath(instPath)), domain = NA, call. = FALSE, immediate. = TRUE) 3: unpackPkg(pkgs[i], pkgnames[i], lib) 2: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, dependencies = dependencies, ...) 1:
Re: [Rd] Sweave Feature Requests and Questions
Hi, see below. On Sat, May 8, 2010 at 7:35 PM, Charlotte Maia mai...@gmail.com wrote: snip Furthermore, any help appreciated here: 1. Does anyone know how to build Sweave documents, using Make, without starting a new instance (or multiple instances) of R, every time Make is called? This can be worked around if you have code sections that don't change at all, put them in a separate file and import them into the main LaTeX document using '\input'. Then use the Makefile to specify the dependencies between the LaTeX files. That way, when you run make the first time, everything will run, but on subsequent calls to make, Sweave will not be called as long as the code in the separate file hasn't changed. 2. Does anyone know a simple workaround to problem 3, without killing the entire Sweave.sty file? Furthermore, I'm temped to stop Sweave from generating all the eps files (I saw an option for this in the Sweave documentation), however I'm concerned it may stop others from building the document, if they use postscript. Then again, do enough people use postscript, to warrant such consideration? I don't think I've used postscript in about 8 years. -roger -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages fails with directory not found
On Tue, 11 May 2010 11:05:45 -0400, Duncan Murdoch murdoch.dun...@gmail.com wrote: I'd appreciate it if you could check whether the problems remain in R-devel, revision 51980 or later. (A build of this revision should be on CRAN by tomorrow, at http://cran.r-project.org/bin/windows/base/rdevel.html .) Thanks for trying to fix this. Here is a cut-and-paste [...edited] from Rgui.exe. Hope it helps. MHP R version 2.12.0 Under development (unstable) (2010-05-11 r51980) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [...] Natural language support but running in an English locale [...] Loading required package: survival Loading required package: stats Loading required package: utils Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' [...] update.packages(ask='graphics') trying URL [...] downloaded 1.0 Mb package 'maps' successfully unpacked and MD5 sums checked package 'rgl' successfully unpacked and MD5 sums checked package 'rJava' successfully unpacked and MD5 sums checked Warning: unable to move temporary installation 'c:\Program Files\R\Library\file390c7e87\rJava' to 'c:\Program Files\R\Library\rJava' package 'strucchange' successfully unpacked and MD5 sums checked package 'svMisc' successfully unpacked and MD5 sums checked package 'tkrplot' successfully unpacked and MD5 sums checked package 'vcd' successfully unpacked and MD5 sums checked package 'XML' successfully unpacked and MD5 sums checked package 'zoo' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\mike.prager\Local Settings\Temp\RtmpyrBgXD\downloaded_packages Warning message: In normalizePath(path) : path[1]=c:\Program Files\R\Library/rJava: The system cannot find the file specified traceback() No traceback available __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages fails with directory not found
On 11/05/2010 6:21 PM, Mike Prager wrote: On Tue, 11 May 2010 11:05:45 -0400, Duncan Murdoch murdoch.dun...@gmail.com wrote: I'd appreciate it if you could check whether the problems remain in R-devel, revision 51980 or later. (A build of this revision should be on CRAN by tomorrow, at http://cran.r-project.org/bin/windows/base/rdevel.html .) Thanks for trying to fix this. Here is a cut-and-paste [...edited] from Rgui.exe. Hope it helps. MHP R version 2.12.0 Under development (unstable) (2010-05-11 r51980) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [...] Natural language support but running in an English locale [...] Loading required package: survival Loading required package: stats Loading required package: utils Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' [...] Was rJava among the packages loaded at the time you tried this? update.packages(ask='graphics') trying URL [...] downloaded 1.0 Mb package 'maps' successfully unpacked and MD5 sums checked package 'rgl' successfully unpacked and MD5 sums checked package 'rJava' successfully unpacked and MD5 sums checked Warning: unable to move temporary installation 'c:\Program Files\R\Library\file390c7e87\rJava' to 'c:\Program Files\R\Library\rJava' After the install was complete, was rJava present in Library? Was it updated? Was the temporary directory file390c7e87 still present? Duncan Murdoch package 'strucchange' successfully unpacked and MD5 sums checked package 'svMisc' successfully unpacked and MD5 sums checked package 'tkrplot' successfully unpacked and MD5 sums checked package 'vcd' successfully unpacked and MD5 sums checked package 'XML' successfully unpacked and MD5 sums checked package 'zoo' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\mike.prager\Local Settings\Temp\RtmpyrBgXD\downloaded_packages Warning message: In normalizePath(path) : path[1]=c:\Program Files\R\Library/rJava: The system cannot find the file specified traceback() No traceback available __ 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
