search for: r_system

Full_Name: Byron Ellis Version: R 1.9.0 (and 2.0.0) OS: Linux (Redhat Fedora Core) Submission from: (NULL) (140.247.241.197) It appears that `R CMD build` cannot handle spaces in the path when building packages for distribution. For instance: [ellis@net-78815 ~/Bayesian Networks]$ R CMD build bnsl * checking for file 'bnsl/DESCRIPTION' ... OK * preparing 'bnsl': * cleaning src *

...log->message("removing junk files"); find(\&unlink_junk_files, $pkgdir); + chdir(dirname($pkgdir)); + my $filename = "${intname}_" . $description->{"Version"} . ".tar"; + my $filepath = &file_path($startdir, $filename); + R_system(join(" ", + ("$tar chf", + &shell_quote_file_path($filepath), + "$pkgname"))); + my $tmpdir = R_tempfile("Rbuild"); + rmtree($tmpdir) if(-d $tmpdir); + mkdir("$tmpdir", 0755) + or...

...dows when there is a cleanup.win. That is, cleanup.win is not run before the archive is created. Here is the code in build.pl that checks for cleanup and runs it before building the archive: if(!$WINDOWS && -x "./cleanup") { $log->message("running cleanup"); R_system("./cleanup"); } But the case where $WINDOWS is true is never addressed. The problem can be resolved by adding: if($WINDOWS && -e "./cleanup.win") { $log->message("running cleanup.win"); R_system("./cleanup.win") } Does this make sens...

...being recovered when R is done. Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of tempdir(). (That should be very rare.) > q("no") Breakpoint 1, R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 311 { (gdb) where #0 R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 #1 0x00005555557c30ec in R_CleanTempDir () at sys-std.c:1178 #2 0x000055...

...rs/braju.com.R/R.basic/R.basic_0.36.tar: No such file or directory HOWEVER, if you do >cd /cygdrive/C/users/braju.com.R/R.basic/ >gzip R.basic_0.36.tar it works. This is also the strategy in the R v1.8.1 build script. In the R v1.9.0 alpha script all gzip calls are on absolute pathnames; R_system("$tar chf $filepath $pkgname"); R_system("gzip -9f $filepath"); cf. system("$tar chf $filepath $pkgname"); chdir($startdir); rmtree($tmpdir); system("gzip -9f $filename"); Modifying the build v1.9.0 alpha to do the latter things works again. More hin...

..., build does not. A fix is below. Also, build.in references Rcmd.exe, which I thought was no longer necessary? Index: build.in =================================================================== --- build.in (revision 36450) +++ build.in (working copy) @@ -434,6 +434,8 @@ if($doit && R_system($cmd)) { $log->error(); $log->print("Installation failed.\n"); + $log->print("Removing '$libdir'\n"); + rmtree($libdir); exit(1); } my $R_LIBS = $ENV{'R_LIBS'};

...----------------------------------------- gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -g -O2 -c sysutils.c -o sysutils.o sysutils.c: In function 'R_system': sysutils.c:289: warning: implicit declaration of function 'WIFEXITED' sysutils.c:289: warning: implicit declaration of function 'WEXITSTATUS' gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra -I. -I../../src/include -I....

...$retval) { # was -f, but want to be able to create such a file $retval = file_path($R::Vars::TMPDIR, $pat . $$ . sprintf("%05d", rand(10**5))); croak "Cannot find unused name for temporary file" if($n++ > 1000); } $retval; } ### * R_system sub R_system { my ($cmd, $Renv) = @_; my $tmpf = R_tempfile(); if($R::Vars::OSTYPE eq "windows") { open(tmpf, "> $tmpf") or die "Error: cannot write to '$tmpf'\n"; print tmpf "$cmd $Renv\n"; close tmpf; $re...

...s done. Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of tempdir(). (That should be very rare.) >> >>> q("no") >> Breakpoint 1, R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 >> 311 { >> (gdb) where >> #0 R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 >> #1 0x00005555557c30ec in R_CleanTempD...

...known object name to predict, or do we need to ask the students to redo all the work with a given model name? (I hope not!) function(L) { fname <- format(Sys.time(), 'Totals_%b%d_%H%M_%S.txt') filesused <- format(Sys.time(), 'Files_%b%d_%H%M_%S.txt') setwd("/Users/gregg/R_system") dire <- getwd() print(dire) flies <- list.files(pattern = "BIOtotal*")# flies instead of files because of FEAR of reserved words!!! for(i in 1:length(flies)) { s <- flies[i] print(i) # print everything for debugging print(s) model <- load(s) print(model) z <- pred...

.../local/lib64/R/bin/build /usr/lib64/R/bin/build 40c40 < my $revision = ' $Rev: 46832 $ '; --- > my $revision = ' $Rev: 45803 $ '; 576,579d570 < if(-r "Makevars") { < $makefiles .= " -f Makevars"; < R_system("${R::Vars::MAKE} $makefiles clean"); < } it produces a warning like $ R-devel CMD build Runuran [...] * DONE (Runuran) * creating vignettes ... OK * cleaning src make: *** No rule to make target `clean'. Stop. * running cleanup * removing junk files * checking fo...

...ert the PS file to a PNG, the postscript drive doesn't wait for ghostscript to finish (under Windows). In the Linux version, the postscript driver does wait for the printing command to finish. Compare the following lines of devPS.c that actually call the "cmd": #ifdef Unix err = R_system(buff); #endif #ifdef Win32 err = runcmd(buff, 0, 0, NULL); #endif RECOMMENDATION: Change runcmd(buff, 0, 0, NULL) to runcmd(buff, 1, 0, NULL) in devPS.c to make the driver wait for the command to finish.

...s+^([A-Za-z]):+/\1/+; - } elsif ($WINDOWS) { - ## workaround for paths in Cygwin tar - $filepath =~ s+^([A-Za-z]):+/cygdrive/\1+; + if($WINDOWS) { + ## workaround for paths in Cygwin tar + $filepath =~ s+^([A-Za-z]):+/cygdrive/\1+; } - R_system(join(" ", ("$tar chf", &shell_quote_file_path($filepath),

...ed when R is done. Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of tempdir(). (That should be very rare.) > > > q("no") > Breakpoint 1, R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 > 311 { > (gdb) where > #0 R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 > #1 0x00005555557c30ec in R_CleanTempDir () at sys-std...

Yesterday I downloaded R-2.2.0.tar.gz, gunzipped and untarred, and did the usual ./configure and make. Everything seemed to go smoothly until it got to the bit about installing recommended packages. It got past ``spatial'' but turned up a fatal error in respect of the ``boot'' package. Here is some of what appeared on the screen:

...TempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of tempdir(). (That should be very rare.) >>>> >>>>> q("no") >>>> Breakpoint 1, R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 >>>> 311 { >>>> (gdb) where >>>> #0 R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 >>>> #1 0x...

...s R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of tempdir(). (That should be very rare.) > >> > >>> q("no") > >> Breakpoint 1, R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 > >> 311 { > >> (gdb) where > >> #0 R_system (command=command at entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311 > >> #1 0x00005555557c...

Dear R-developers, Some of the more fat scripts (50+ GB mem used by R) that I am running, when they finish they do quit with q("no", status=0) Quite often it happens that there is an extra stderr output produced at the very end which looks like this: Warning message: In .Internal(quit(save, status, runLast)) : system call failed: Cannot allocate memory Is there any way to avoid this

I think you had to be using an install log to get that message. It is true that R_system($cmd) is not returning an error code, and I've fixed that. On Thu, 15 Apr 2004 ligges@statistik.uni-dortmund.de wrote: > I just post it not to forget - will try to contribute a fix. > > Example: CDNmoney_2003.9-2.tar.gz (in the archives section of CRAN) > [There is another prob...

I have an R library which uses identify() and system(com="xterm -e less /a/corresponding/file") to view files when I click on an x11() plot. I can successfully resize the xterm on Linux (i486) and Macos 10.4 (G4 and G5), but NOT Macos 10.4 (Intel). For example, on a new mac pro: # in a terminal,xterm,iterm,etc: xterm -e "printenv | less" # the resulting xterm resizes