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hb@maths.lth.se

2003-Apr-22 17:24 UTC

[Rd] zip.unpack() crashes R (PR#2818)

Full_Name: Henrik Bengtsson
Version: R v1.7.0
OS: WinXP Pro
Submission from: (NULL) (130.235.2.229)


There seems to be an upper limit of the number of files (approx 1000 files) a
zip-file can contain when unpacking it with zip.unpack(). This results in an R
crash. This bug is urgent since install.packages() relies on zip.unpack() and
too big packages/bundles won't install with the current R v1.7.0 for
Windows.

The following R script creates a directory with N files and zips it and tries to
unpack it again. Try with a large number on N (N=1003 is probably enough) and R
will crash. The traceback from Dr. Mingw is pasted at the end.

# 1. Running the script several times with N = 900 crashes R or generates 
# the error:
# Error in zip.unpack("dir.zip", "c:/tmp") :
#        can not set length of non-vector
# 2. Running the script twice with N = 1002 crashes R
# 3. Running the script twice with N = 1003 crashes R (every time?)
# 4. Running the script twice with N = 2000 crashes R (every time!)
N <- 1003

# Create an directory with N files
dest <- "dir"
dir.create(dest)
files <- list.files(dest)
nMissing <- (N - length(files))
if (nMissing > 0) {
  idx <- (length(files)+1):N
  filename <- sapply(as.integer(idx), FUN=sprintf,
fmt="file%05d.txt")
  pathname <- paste(dest, filename, sep="/")
  for (k in seq(pathname))
    cat(file=pathname[k], 0)
}

# Create a zip archive of the directory
zipper <- "C:/cygwin/bin/jar -cfM"
cmd <- paste(zipper, " ", dest, ".zip", " ",
dest, sep="")
system(cmd)

# Unse zip.unpack(), which is used by install.packages(), to unpack it.
zip.unpack("dir.zip", "c:/tmp")


# From Dr. Mingw:
# Rterm.exe caused an Access Violation at location 004d2a04 in module R.dll
Writing to location 0235f4cc.
# 
# Registers:
# eax=0235f4c8 ebx=0235e508 ecx=0235a511 edx=00000fc0 esi=00637b90 edi=80000000
# eip=004d2a04 esp=0022c840 ebp=0022c868 iopl=0         nv up ei pl nz na po nc
# cs=001b  ss=0023  ds=0023  es=0023  fs=0038  gs=0000             efl=00000206
# 
# Call stack:
# 004D2A04  R.dll:004D2A04  malloc
# 0054FEFA  R.dll:0054FEFA  Rf_allocVector
# 0051AA10  R.dll:0051AA10  call_S
# 0051ABB7  R.dll:0051ABB7  call_S
# 0051AF18  R.dll:0051AF18  do_int_unzip
# 00559594  R.dll:00559594  do_internal
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052BA52  R.dll:0052BA52  do_begin
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052BA52  R.dll:0052BA52  do_begin
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052BA52  R.dll:0052BA52  do_begin
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052A6B5  R.dll:0052A6B5  Rf_applyClosure
# 0052A1D7  R.dll:0052A1D7  Rf_eval
# 0052CCE6  R.dll:0052CCE6  do_eval
# 00559594  R.dll:00559594  do_internal
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052A6B5  R.dll:0052A6B5  Rf_applyClosure
# 0052A1D7  R.dll:0052A1D7  Rf_eval
# 0052C2D5  R.dll:0052C2D5  do_set
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052BA52  R.dll:0052BA52  do_begin
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052B427  R.dll:0052B427  do_for
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052BA52  R.dll:0052BA52  do_begin
# 0052A3C8  R.dll:0052A3C8  Rf_eval
# 0052A6B5  R.dll:0052A6B5  Rf_applyClosure
# 0052A1D7  R.dll:0052A1D7  Rf_eval
# 0054996E  R.dll:0054996E  Rf_ReplIteration
# 00549F72  R.dll:00549F72  Rf_ReplIteration
# 0054AA76  R.dll:0054AA76  run_Rmainloop
# 00401571  Rterm.exe:00401571
# 0040141E  Rterm.exe:0040141E
# 004017B3  Rterm.exe:004017B3
# 00401165  Rterm.exe:00401165
# 00401013  Rterm.exe:00401013
# 77E814C7  kernel32.dll:77E814C7  GetCurrentDirectoryW


# Platform (a fresh R installation):
#  > R.version
#  	    _
#  platform i386-pc-mingw32
#  arch     i386
#  os       mingw32
#  system   i386, mingw32
#  status
#  major    1
#  minor    7.0
#  year     2003
#  month    04
#  day      16
#  language R

Henrik Bengtsson

2003-Apr-22 17:30 UTC

head link

[Rd] zip.unpack() crashes R (PR#2818)

Sorry for the reposting of PR #2818 (PR #2820 and PR #2821). It's
because I did reload in my browser after posting the bug report. In
other words, PR #2818 == PR #2820 == PR #2821.

/Henrik
> -----Original Message-----
> From: r-devel-bounces@stat.math.ethz.ch 
> [mailto:r-devel-bounces@stat.math.ethz.ch] On Behalf Of 
> hb@maths.lth.se
> Sent: den 22 april 2003 17:23
> To: r-devel@stat.math.ethz.ch
> Cc: R-bugs@biostat.ku.dk
> Subject: [Rd] zip.unpack() crashes R (PR#2818)
> 
> 
> Full_Name: Henrik Bengtsson
> Version: R v1.7.0
> OS: WinXP Pro
> Submission from: (NULL) (130.235.2.229)
> 
> 
> There seems to be an upper limit of the number of files 
> (approx 1000 files) a zip-file can contain when unpacking it 
> with zip.unpack(). This results in an R crash. This bug is 
> urgent since install.packages() relies on zip.unpack() and 
> too big packages/bundles won't install with the current R 
> v1.7.0 for Windows.
> 
> The following R script creates a directory with N files and 
> zips it and tries to unpack it again. Try with a large number 
> on N (N=1003 is probably enough) and R will crash. The 
> traceback from Dr. Mingw is pasted at the end.
> 
> # 1. Running the script several times with N = 900 crashes R 
> or generates 
> # the error:
> # Error in zip.unpack("dir.zip", "c:/tmp") :
> #        can not set length of non-vector
> # 2. Running the script twice with N = 1002 crashes R
> # 3. Running the script twice with N = 1003 crashes R (every 
> time?) # 4. Running the script twice with N = 2000 crashes R 
> (every time!) N <- 1003
> 
> # Create an directory with N files
> dest <- "dir"
> dir.create(dest)
> files <- list.files(dest)
> nMissing <- (N - length(files))
> if (nMissing > 0) {
>   idx <- (length(files)+1):N
>   filename <- sapply(as.integer(idx), FUN=sprintf,
fmt="file%05d.txt")
>   pathname <- paste(dest, filename, sep="/")
>   for (k in seq(pathname))
>     cat(file=pathname[k], 0)
> }
> 
> # Create a zip archive of the directory
> zipper <- "C:/cygwin/bin/jar -cfM"
> cmd <- paste(zipper, " ", dest, ".zip", "
", dest, sep="")
> system(cmd)
> 
> # Unse zip.unpack(), which is used by install.packages(), to 
> unpack it. zip.unpack("dir.zip", "c:/tmp")
> 
> 
> # From Dr. Mingw:
> # Rterm.exe caused an Access Violation at location 004d2a04 
> in module R.dll Writing to location 0235f4cc. # 
> # Registers:
> # eax=0235f4c8 ebx=0235e508 ecx=0235a511 edx=00000fc0 
> esi=00637b90 edi=80000000
> # eip=004d2a04 esp=0022c840 ebp=0022c868 iopl=0         nv up 
> ei pl nz na po nc
> # cs=001b  ss=0023  ds=0023  es=0023  fs=0038  gs=0000        
>      efl=00000206
> # 
> # Call stack:
> # 004D2A04  R.dll:004D2A04  malloc
> # 0054FEFA  R.dll:0054FEFA  Rf_allocVector
> # 0051AA10  R.dll:0051AA10  call_S
> # 0051ABB7  R.dll:0051ABB7  call_S
> # 0051AF18  R.dll:0051AF18  do_int_unzip
> # 00559594  R.dll:00559594  do_internal
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052BA52  R.dll:0052BA52  do_begin
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052BA52  R.dll:0052BA52  do_begin
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052BA52  R.dll:0052BA52  do_begin
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052A6B5  R.dll:0052A6B5  Rf_applyClosure
> # 0052A1D7  R.dll:0052A1D7  Rf_eval
> # 0052CCE6  R.dll:0052CCE6  do_eval
> # 00559594  R.dll:00559594  do_internal
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052A6B5  R.dll:0052A6B5  Rf_applyClosure
> # 0052A1D7  R.dll:0052A1D7  Rf_eval
> # 0052C2D5  R.dll:0052C2D5  do_set
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052BA52  R.dll:0052BA52  do_begin
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052B427  R.dll:0052B427  do_for
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052BA52  R.dll:0052BA52  do_begin
> # 0052A3C8  R.dll:0052A3C8  Rf_eval
> # 0052A6B5  R.dll:0052A6B5  Rf_applyClosure
> # 0052A1D7  R.dll:0052A1D7  Rf_eval
> # 0054996E  R.dll:0054996E  Rf_ReplIteration
> # 00549F72  R.dll:00549F72  Rf_ReplIteration
> # 0054AA76  R.dll:0054AA76  run_Rmainloop
> # 00401571  Rterm.exe:00401571
> # 0040141E  Rterm.exe:0040141E
> # 004017B3  Rterm.exe:004017B3
> # 00401165  Rterm.exe:00401165
> # 00401013  Rterm.exe:00401013
> # 77E814C7  kernel32.dll:77E814C7  GetCurrentDirectoryW
> 
> 
> # Platform (a fresh R installation):
> #  > R.version
> #  	    _
> #  platform i386-pc-mingw32
> #  arch     i386
> #  os       mingw32
> #  system   i386, mingw32
> #  status
> #  major    1
> #  minor    7.0
> #  year     2003
> #  month    04
> #  day      16
> #  language R
> 
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list 
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-devel
> 
>

Peter Dalgaard BSA

2003-Apr-22 19:07 UTC

head link

[Rd] zip.unpack() crashes R (PR#2818)

hb@maths.lth.se writes:
> # 1. Running the script several times with N = 900 crashes R or generates 
> # the error:
> # Error in zip.unpack("dir.zip", "c:/tmp") :
> #        can not set length of non-vector
> # 2. Running the script twice with N = 1002 crashes R
> # 3. Running the script twice with N = 1003 crashes R (every time?)
> # 4. Running the script twice with N = 2000 crashes R (every time!)
> N <- 1003
....> # Unse zip.unpack(), which is used by install.packages(), to unpack it.
> zip.unpack("dir.zip", "c:/tmp")
Reproducible on Linux with

.Internal(int.unzip("dir.zip",NULL, "/tmp"))

instead of zip.unpack.

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907

Prof Brian Ripley

2003-Apr-24 18:49 UTC

head link

[Rd] zip.unpack() crashes R (PR#2818)

On Tue, 22 Apr 2003 hb@maths.lth.se wrote:
> Full_Name: Henrik Bengtsson
> Version: R v1.7.0
> OS: WinXP Pro
> Submission from: (NULL) (130.235.2.229)
> 
> 
> There seems to be an upper limit of the number of files (approx 1000 files)
a
Yes, 500 topics.
> zip-file can contain when unpacking it with zip.unpack(). This results in
an R
> crash. This bug is urgent since install.packages() relies on zip.unpack()
and
> too big packages/bundles won't install with the current R v1.7.0 for
Windows.
Whyever should a R package have over 1000 files?
I think you are not understanding how to use the --use-zip options.

Also, look at options("unzip").

Why is this bug `urgent':  it has been around for 14 months, and no one
else has encountered a problem?

-- 
Brian D. Ripley,                  ripley@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, UK                Fax:  +44 1865 272595

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