Henrik Bengtsson
2005-Jun-27 14:38 UTC
[Rd] R v2.1.1 for Windows and "non-reproducible" crashes
Hi,
R v2.1.1 patched (2005-05-26) for Windows crashes. The sympotoms are
like "memory leakage". The patched version from two days ago crashes
at
a different position in R CMD check compared to todays version.
A "REPRODUCIBLE" EXAMPLE:
Unfortunately, I cannot create a minimal code example reproducing the
crash, but here is at least a simple way to reproduce it:
1. Make sure you run R v2.1.1 patched
2. Start R
3. install.packages("R.oo",
contriburl="http://www.maths.lth.se/help/R")
[This is a version built with R v2.1.0, because I cannot make the
package pass R CMD check on v2.1.1 because of the crashes]
4. Cut'n'paste the following example from ?Rdoc to the R prompt:
library(R.oo)
author <- "Henrik Bengtsson, \url{http://www.braju.com/R/}"
rdocFile <- system.file("misc", "Exception.R",
package="R.oo")
file.show(rdocFile)
destPath <- tempdir()
Rdoc$compile(rdocFile, destPath=destPath)
rdFiles <- list.files(destPath, full.names=TRUE)
print(rdFiles)
file.show(rdFiles[1])
file.remove(rdFiles)
For me it crashes when it gets to the Rdoc$compile() line and Dr. Mingw
reports:
Rterm.exe caused an Access Violation at location 7c911e58 in module
ntdll.dll Reading from location 52474f52.
Registers:
eax=003efa18 ebx=003e0000 ecx=52474f52 edx=502f3a43 esi=003efa10
edi=003efa48
eip=7c911e58 esp=00228c10 ebp=00228c1c iopl=0 nv up ei pl zr na
po nc
cs=001b ss=0023 ds=0023 es=0023 fs=003b gs=0000
efl=00000246
Call stack:
7C911E58 ntdll.dll:7C911E58 RtlInitializeCriticalSection
7C910D5C ntdll.dll:7C910D5C wcsncpy
77C2C2DE msvcrt.dll:77C2C2DE free
1004BFB0 R.dll:1004BFB0 do_isseekable
1004C051 R.dll:1004C051 con_close
1004D33E R.dll:1004D33E do_close
100A8E41 R.dll:100A8E41 do_internal
1008494A R.dll:1008494A Rf_eval
10085595 R.dll:10085595 Rf_evalList
10084993 R.dll:10084993 Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100A9361 R.dll:100A9361 do_internal
100A99A5 R.dll:100A99A5 Rf_usemethod
100A9E1A R.dll:100A9E1A do_usemethod
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10051EE9 R.dll:10051EE9 Rf_endcontext
1008751F R.dll:1008751F Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10086305 R.dll:10086305 do_set
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100A9361 R.dll:100A9361 do_internal
100A99A5 R.dll:100A99A5 Rf_usemethod
100A9E1A R.dll:100A9E1A do_usemethod
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10086305 R.dll:10086305 do_set
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
10084671 R.dll:10084671 Rf_eval
1008487C R.dll:1008487C Rf_eval
10084671 R.dll:10084671 Rf_eval
1008487C R.dll:1008487C Rf_eval
10084671 R.dll:10084671 Rf_eval
1008487C R.dll:1008487C Rf_eval
100852A5 R.dll:100852A5 Rf_evalListKeepMissing
100853DD R.dll:100853DD do_return
1008494A R.dll:1008494A Rf_eval
10084671 R.dll:10084671 Rf_eval
1008487C R.dll:1008487C Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10086305 R.dll:10086305 do_set
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
1008494A R.dll:1008494A Rf_eval
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10086305 R.dll:10086305 do_set
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
10086A18 R.dll:10086A18 do_for
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100A9361 R.dll:100A9361 do_internal
100A99A5 R.dll:100A99A5 Rf_usemethod
100A9E1A R.dll:100A9E1A do_usemethod
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10086305 R.dll:10086305 do_set
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10084671 R.dll:10084671 Rf_eval
1008487C R.dll:1008487C Rf_eval
10085595 R.dll:10085595 Rf_evalList
100A8F0F R.dll:100A8F0F do_internal
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10085012 R.dll:10085012 do_eval
100A8E41 R.dll:100A8E41 do_internal
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100866A2 R.dll:100866A2 do_while
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
10086A18 R.dll:10086A18 do_for
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
10086305 R.dll:10086305 do_set
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
10086A18 R.dll:10086A18 do_for
1008494A R.dll:1008494A Rf_eval
100863D5 R.dll:100863D5 do_begin
1008494A R.dll:1008494A Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
100875AB R.dll:100875AB Rf_applyClosure
100846E0 R.dll:100846E0 Rf_eval
1009D5E6 R.dll:1009D5E6 Rf_ReplIteration
1009D717 R.dll:1009D717 Rf_ReplIteration
1009D997 R.dll:1009D997 run_Rmainloop
0040144C Rterm.exe:0040144C
004012C5 Rterm.exe:004012C5
004016BA Rterm.exe:004016BA
004011E7 Rterm.exe:004011E7
00401238 Rterm.exe:00401238
7C816D4F kernel32.dll:7C816D4F RegisterWaitForInputIdle
Sometimes it just give an error about an invalid regular expression;
then rerun the line for it to crash, e.g.
> Rdoc$compile(rdocFile, destPath=destPath)
Loading required package: tools
Error in regexpr(pattern, text, extended, fixed, useBytes) :
invalid regular expression '^@classhierarchy'
Then redo the Rdoc$compile() line and R will crash.
Also, note that the regular expression pattern in the error report from
regexpr() about "invalid regular expression '^@alias'" is
valid, because
trying it in R you get
> regexpr("^@classhierarchy", "@classhierarchy")
[1] 1
attr(,"match.length")
[1] 15
I have also received messages about "invalid regular expression
''", but
I am sure I do not use empty regular expressions anywhere.
I am pretty sure it is not the R.oo package itself, because nothing much
has changed and the package has passed the R CMD check for many R
versions including R v2.1.0 patched (2005-05-09). The crashed to not
occur on the R v2.1.0 patched version.
Has anyone else noticed this? Can you reproduce the above, or is it
just my Windows installation? If I figure out more on this myself, I'll
get back to you.
My system is Windows XP Pro English SP2 with
> R.Version()
$platform
[1] "i386-pc-mingw32"
$arch
[1] "i386"
$os
[1] "mingw32"
$system
[1] "i386, mingw32"
$status
[1] "Patched"
$major
[1] "2"
$minor
[1] "1.1"
$year
[1] "2005"
$month
[1] "06"
$day
[1] "26"
$language
[1] "R"
Best
Henrik
Henrik Bengtsson
2005-Jun-27 14:44 UTC
[Rd] R v2.1.1 for Windows and "non-reproducible" crashes
Henrik Bengtsson wrote:> Hi, > > R v2.1.1 patched (2005-05-26) for Windows crashes. The sympotoms are > like "memory leakage". The patched version from two days ago crashes at > a different position in R CMD check compared to todays version.Sorry for being unclear; the "R CMD check" refers to R CMD check for my R.oo package and is just an example.> A "REPRODUCIBLE" EXAMPLE: > Unfortunately, I cannot create a minimal code example reproducing the > crash, but here is at least a simple way to reproduce it: > > 1. Make sure you run R v2.1.1 patched > 2. Start R > 3. install.packages("R.oo", contriburl="http://www.maths.lth.se/help/R") > [This is a version built with R v2.1.0, because I cannot make the > package pass R CMD check on v2.1.1 because of the crashes] > 4. Cut'n'paste the following example from ?Rdoc to the R prompt: > library(R.oo) > author <- "Henrik Bengtsson, \url{http://www.braju.com/R/}" > rdocFile <- system.file("misc", "Exception.R", package="R.oo") > file.show(rdocFile) > destPath <- tempdir() > Rdoc$compile(rdocFile, destPath=destPath) > rdFiles <- list.files(destPath, full.names=TRUE) > print(rdFiles) > file.show(rdFiles[1]) > file.remove(rdFiles) > > For me it crashes when it gets to the Rdoc$compile() line and Dr. Mingw > reports: > > Rterm.exe caused an Access Violation at location 7c911e58 in module > ntdll.dll Reading from location 52474f52. > > Registers: > eax=003efa18 ebx=003e0000 ecx=52474f52 edx=502f3a43 esi=003efa10 > edi=003efa48 > eip=7c911e58 esp=00228c10 ebp=00228c1c iopl=0 nv up ei pl zr na > po nc > cs=001b ss=0023 ds=0023 es=0023 fs=003b gs=0000 > efl=00000246 > > Call stack: > 7C911E58 ntdll.dll:7C911E58 RtlInitializeCriticalSection > 7C910D5C ntdll.dll:7C910D5C wcsncpy > 77C2C2DE msvcrt.dll:77C2C2DE free > 1004BFB0 R.dll:1004BFB0 do_isseekable > 1004C051 R.dll:1004C051 con_close > 1004D33E R.dll:1004D33E do_close > 100A8E41 R.dll:100A8E41 do_internal > 1008494A R.dll:1008494A Rf_eval > 10085595 R.dll:10085595 Rf_evalList > 10084993 R.dll:10084993 Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100A9361 R.dll:100A9361 do_internal > 100A99A5 R.dll:100A99A5 Rf_usemethod > 100A9E1A R.dll:100A9E1A do_usemethod > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10051EE9 R.dll:10051EE9 Rf_endcontext > 1008751F R.dll:1008751F Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10086305 R.dll:10086305 do_set > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100A9361 R.dll:100A9361 do_internal > 100A99A5 R.dll:100A99A5 Rf_usemethod > 100A9E1A R.dll:100A9E1A do_usemethod > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10086305 R.dll:10086305 do_set > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 10084671 R.dll:10084671 Rf_eval > 1008487C R.dll:1008487C Rf_eval > 10084671 R.dll:10084671 Rf_eval > 1008487C R.dll:1008487C Rf_eval > 10084671 R.dll:10084671 Rf_eval > 1008487C R.dll:1008487C Rf_eval > 100852A5 R.dll:100852A5 Rf_evalListKeepMissing > 100853DD R.dll:100853DD do_return > 1008494A R.dll:1008494A Rf_eval > 10084671 R.dll:10084671 Rf_eval > 1008487C R.dll:1008487C Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10086305 R.dll:10086305 do_set > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 1008494A R.dll:1008494A Rf_eval > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10086305 R.dll:10086305 do_set > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 10086A18 R.dll:10086A18 do_for > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100A9361 R.dll:100A9361 do_internal > 100A99A5 R.dll:100A99A5 Rf_usemethod > 100A9E1A R.dll:100A9E1A do_usemethod > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10086305 R.dll:10086305 do_set > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10084671 R.dll:10084671 Rf_eval > 1008487C R.dll:1008487C Rf_eval > 10085595 R.dll:10085595 Rf_evalList > 100A8F0F R.dll:100A8F0F do_internal > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10085012 R.dll:10085012 do_eval > 100A8E41 R.dll:100A8E41 do_internal > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100866A2 R.dll:100866A2 do_while > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 10086A18 R.dll:10086A18 do_for > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 10086305 R.dll:10086305 do_set > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 10086A18 R.dll:10086A18 do_for > 1008494A R.dll:1008494A Rf_eval > 100863D5 R.dll:100863D5 do_begin > 1008494A R.dll:1008494A Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 100875AB R.dll:100875AB Rf_applyClosure > 100846E0 R.dll:100846E0 Rf_eval > 1009D5E6 R.dll:1009D5E6 Rf_ReplIteration > 1009D717 R.dll:1009D717 Rf_ReplIteration > 1009D997 R.dll:1009D997 run_Rmainloop > 0040144C Rterm.exe:0040144C > 004012C5 Rterm.exe:004012C5 > 004016BA Rterm.exe:004016BA > 004011E7 Rterm.exe:004011E7 > 00401238 Rterm.exe:00401238 > 7C816D4F kernel32.dll:7C816D4F RegisterWaitForInputIdle > > Sometimes it just give an error about an invalid regular expression; > then rerun the line for it to crash, e.g. > > > Rdoc$compile(rdocFile, destPath=destPath) > Loading required package: tools > Error in regexpr(pattern, text, extended, fixed, useBytes) : > invalid regular expression '^@classhierarchy' > > Then redo the Rdoc$compile() line and R will crash. > > Also, note that the regular expression pattern in the error report from > regexpr() about "invalid regular expression '^@alias'" is valid, because > trying it in R you get > > > regexpr("^@classhierarchy", "@classhierarchy") > [1] 1 > attr(,"match.length") > [1] 15 > > I have also received messages about "invalid regular expression ''", but > I am sure I do not use empty regular expressions anywhere. > > I am pretty sure it is not the R.oo package itself, because nothing much > has changed and the package has passed the R CMD check for many R > versions including R v2.1.0 patched (2005-05-09). The crashed to not > occur on the R v2.1.0 patched version. > > > Has anyone else noticed this? Can you reproduce the above, or is it > just my Windows installation? If I figure out more on this myself, I'll > get back to you. > > My system is Windows XP Pro English SP2 with > > > R.Version() > $platform > [1] "i386-pc-mingw32" > > $arch > [1] "i386" > > $os > [1] "mingw32" > > $system > [1] "i386, mingw32" > > $status > [1] "Patched" > > $major > [1] "2" > > $minor > [1] "1.1" > > $year > [1] "2005" > > $month > [1] "06" > > $day > [1] "26" > > $language > [1] "R" > > Best > > Henrik > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >
Recently, I notice strange things when I try to build R 2.1.1 on Windows XP. I downloaded and unpacked. R-2.1.1.tar.gz. All the tools are in place. I get as far as building the installer, and then the following happens: perl JRins.pl rw2011 rw2011 "C:/Program Files/Inno Setup 5/iscc" R.iss > rw2011.log 2>&1 make[2]: Leaving directory `/cygdrive/c/devel/R/R-2.1.1/src/gnuwin32/installer' make[2]: Entering directory `/cygdrive/c/devel/R/R-2.1.1/src/gnuwin32/installer' rm -rf R.iss Rsmall.iss *.log rw2011 rm: cannot remove directory `rw2011/library/base/html': Directory not empty rm: cannot remove directory `rw2011/library/tcltk/Meta': Directory not empty make[2]: *** [clean] Error 1 make[2]: Leaving directory `/cygdrive/c/devel/R/R-2.1.1/src/gnuwin32/installer' make[1]: *** [rinstaller] Error 2 make[1]: Leaving directory `/cygdrive/c/devel/R/R-2.1.1/src/gnuwin32' make: *** [distribution] Error 2 Looking into the two supposedly nonempty directories I see that in fact that are empty. Of course, I only can look a little bit later, so this might be a timing issue. Has anyone experienced similar problems? This effect is somewhat random. The supposedly nonempty directories change from build attempt to build attempt. So far, this has not happened when I build R-patched and R-devel which I update from SVN. Erich Neuwirth