Bug#353723: marked as done (python2.3-rpy: library path does not allow loading all R modules)

[Debian Bug Tracking System]

Your message dated Tue, 21 Feb 2006 08:27:03 -0600
with message-id <[EMAIL PROTECTED]>
and subject line Bug#353723: python2.3-rpy: library path does not allow loading 
     all R modules
has caused the attached Bug report to be marked as done.

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--- Begin Message ---

Package: python2.3-rpy
Version: 0.4.1-4
Severity: normal

Hello,

I had a problem with rpy not finding a needed module. I did the
following:

$ python
Python 2.3.5 (#2, May  4 2005, 08:51:39)
[GCC 3.3.5 (Debian 1:3.3.5-12)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
>>> from rpy import r
>>> m=r('log(y)~x')
>>> f=rpy.with_mode(0,r('lm'))(m,{'x':[1,2,3],'y':[2,4,8]})
>>> r('summary')(f)
Warning message:
unable to load shared library '/usr/lib/R/modules/lapack.so':
  libRlapack.so: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier
ou rép
ertoire de ce type
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
rpy.RException: Error in La.chol2inv(x, size) : lapack routines cannot be
loaded

>>>

By contrast, it works in R:

$ R

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.0  (2005-04-18), ISBN 3-900051-07-0

... ( lines cut ) ...

Type 'q()' to quit R.

> m=log(y)~x
> data <- data.frame(x=c(1,2,3),y=c(2,4,8))
> f=lm(m,data=data)
> summary(f)

Call:
lm(formula = m, data = data)

... ( lines cut ) ...

F-statistic: 4.679e+32 on 1 and 1 DF,  p-value: < 2.2e-16

>

When using strace (log attached), it looks like rpy finds lapack.so
in /usr/lib/R/modules/, but then looks for  libRlapack.so in the
library path, which does not include /usr/lib/R/lib/.

The following works around the problem:

$ export LD_LIBRARY_PATH=/usr/lib/R/lib/:$LD_LIBRARY_PATH
$ python
... same as before, but it works now ...

Hope this information will help making this work out of the box.
Cheers,
BC

-- System Information:
Debian Release: 3.1
  APT prefers unstable
  APT policy: (88, 'unstable'), (88, 'testing'), (1, 'experimental')
Architecture: i386 (i686)
Kernel: Linux 2.6.6-1-686
Locale: LANG=fr_FR, LC_CTYPE=fr_FR (charmap=ISO-8859-1)

Versions of packages python2.3-rpy depends on:
ii  libc6                         2.3.5-8    GNU C Library: Shared
libraries an
ii  python2.3                     2.3.5-3    An interactive high-level
object-o
ii  python2.3-numeric             23.8-1     Numerical (matrix-oriented)
Mathem
ii  r-base-core                   2.1.0-1    GNU R core of statistical
computin

-- no debconf information
$ strace python

...( relevant part only )...

open("/usr/lib/R/modules/lapack.so", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\200\34"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0644, st_size=44344, ...}) = 0
old_mmap(NULL, 47404, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 
0x41140000
old_mmap(0x4114b000, 4096, PROT_READ|PROT_WRITE, 
MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0xa000) = 0x4114b000
close(3)                                = 0
open("tls/i686/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
open("tls/i686/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("tls/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or directory)
open("tls/libRlapack.so", O_RDONLY)     = -1 ENOENT (No such file or directory)
open("i686/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
open("i686/libRlapack.so", O_RDONLY)    = -1 ENOENT (No such file or directory)
open("cmov/libRlapack.so", O_RDONLY)    = -1 ENOENT (No such file or directory)
open("libRlapack.so", O_RDONLY)         = -1 ENOENT (No such file or directory)
open("/usr/local/lib/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
open("/data/Science/bin/additional-lib/libRlapack.so", O_RDONLY) = -1 ENOENT 
(No such file or directory)
open("/etc/ld.so.cache", O_RDONLY)      = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=77836, ...}) = 0
old_mmap(NULL, 77836, PROT_READ, MAP_PRIVATE, 3, 0) = 0x411fc000
close(3)                                = 0
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
open("/lib/tls/i686/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/lib/tls/i686/cmov", 0xbfffbf00) = -1 ENOENT (No such file or directory)
open("/lib/tls/i686/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/lib/tls/i686", 0xbfffbf00)     = -1 ENOENT (No such file or directory)
open("/lib/tls/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/lib/tls/cmov", 0xbfffbf00)     = -1 ENOENT (No such file or directory)
open("/lib/tls/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/lib/tls", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
open("/lib/i686/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/lib/i686/cmov", 0xbfffbf00)    = -1 ENOENT (No such file or directory)
open("/lib/i686/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/lib/i686", 0xbfffbf00)         = -1 ENOENT (No such file or directory)
open("/lib/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/lib/cmov", 0xbfffbf00)         = -1 ENOENT (No such file or directory)
open("/lib/libRlapack.so", O_RDONLY)    = -1 ENOENT (No such file or directory)
stat64("/lib", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
open("/usr/lib/tls/i686/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such 
file or directory)
stat64("/usr/lib/tls/i686/cmov", 0xbfffbf00) = -1 ENOENT (No such file or 
directory)
open("/usr/lib/tls/i686/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/usr/lib/tls/i686", 0xbfffbf00) = -1 ENOENT (No such file or directory)
open("/usr/lib/tls/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/usr/lib/tls/cmov", 0xbfffbf00) = -1 ENOENT (No such file or directory)
open("/usr/lib/tls/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/usr/lib/tls", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
open("/usr/lib/i686/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/usr/lib/i686/cmov", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
open("/usr/lib/i686/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/usr/lib/i686", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
open("/usr/lib/cmov/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or 
directory)
stat64("/usr/lib/cmov", 0xbfffbf00)     = -1 ENOENT (No such file or directory)
open("/usr/lib/libRlapack.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib", {st_mode=S_IFDIR|0755, st_size=61440, ...}) = 0
munmap(0x411fc000, 77836)               = 0
munmap(0x41140000, 47404)               = 0
open("/usr/share/locale/locale.alias", O_RDONLY) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=2582, ...}) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 
0x41140000
read(3, "# Locale name alias data base.\n#"..., 4096) = 2582
read(3, "", 4096)                       = 0
close(3)                                = 0
munmap(0x41140000, 4096)                = 0
open("/usr/share/locale/fr_FR/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No 
such file or directory)
open("/usr/share/locale/fr/LC_MESSAGES/libc.mo", O_RDONLY) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=120881, ...}) = 0
mmap2(NULL, 120881, PROT_READ, MAP_PRIVATE, 3, 0) = 0x41b47000
close(3)                                = 0
open("/usr/lib/R/share/locale/fr_FR/LC_MESSAGES/R.mo", O_RDONLY) = -1 ENOENT 
(No such file or directory)
open("/usr/lib/R/share/locale/fr/LC_MESSAGES/R.mo", O_RDONLY) = -1 ENOENT (No 
such file or directory)
write(2, "Warning message:\n", 17Warning message:
)      = 17
write(2, "unable to load shared library \'/"..., 162unable to load shared 
library '/usr/lib/R/modules/lapack.so':
  libRlapack.so: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier ou 
répertoire de ce type 
) = 162

--- End Message ---

--- Begin Message ---

On 21 February 2006 at 13:41, [EMAIL PROTECTED] wrote:
| Hello,
| 
| thanks for your quick answer. I am in fact running stable, with a few
| packages from testing, that's the reason I am using older versions.

Mixed systems can have their surprises, yes. That said, I think they are a
good compromise.

| with python2.3-rpy, version 0.4.1-4 (from stable), ldd gives me:
| 
| $ ldd /usr/lib/python2.3/site-packages/_rpy.so
|         linux-gate.so.1 =>  (0xffffe000)
|         libR.so => /usr/lib/R/lib/libR.so (0x40009000)
|         libpthread.so.0 => /lib/tls/libpthread.so.0 (0x40263000)
|         libc.so.6 => /lib/tls/libc.so.6 (0x40275000)
|         libblas.so.3 => /usr/lib/atlas/libblas.so.3 (0x403ac000)
|         libg2c.so.0 => /usr/lib/libg2c.so.0 (0x406f5000)
|         libm.so.6 => /lib/tls/libm.so.6 (0x40713000)
|         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x40739000)
|         libreadline.so.5 => /lib/libreadline.so.5 (0x40744000)
|         libpcre.so.3 => /usr/lib/libpcre.so.3 (0x40771000)
|         libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x40781000)
|         libz.so.1 libRlapack.so=> /usr/lib/libz.so.1 (0x40790000)
|         libdl.so.2 => /lib/tls/libdl.so.2 (0x407a2000)
|         /lib/ld-linux.so.2 (0x80000000)
|         libncurses.so.5 => /lib/libncurses.so.5 (0x407a7000)
| 
| No libRlapack.so.
| 
| After upgrading python2.3-rpy and r-base-core to the versions in testing
| (the same as yours: 0.4.6-3 and 2.2.1-6), I get:
| 
| $ ldd /usr/lib/python2.3/site-packages/_rpy2021.so
|         linux-gate.so.1 =>  (0xffffe000)
|         libR.so => /usr/lib/R/lib/libR.so (0x4000a000)
|         libRlapack.so => /usr/lib/R/lib/libRlapack.so (0x4025c000)
|         libpthread.so.0 => /lib/tls/libpthread.so.0 (0x40417000)
|         libc.so.6 => /lib/tls/libc.so.6 (0x40429000)
|         libblas.so.3 => /usr/lib/atlas/libblas.so.3 (0x40560000)
|         libg2c.so.0 => /usr/lib/libg2c.so.0 (0x408a9000)
|         libm.so.6 => /lib/tls/libm.so.6 (0x408d2000)
|         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x408f7000)
|         libreadline.so.5 => /lib/libreadline.so.5 (0x40902000)
|         libpcre.so.3 => /usr/lib/libpcre.so.3 (0x40932000)
|         libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x40942000)
|         libz.so.1 => /usr/lib/libz.so.1 (0x40951000)
|         libdl.so.2 => /lib/tls/libdl.so.2 (0x40964000)
|         /lib/ld-linux.so.2 (0x80000000)
|         libncurses.so.5 => /lib/libncurses.so.5 (0x40968000)
| 
| and the program now works as expected. I checked that python2.4-rpy also
| works.

So I am closing the bug report. Thanks for the follow-up from your end.

| So it looks that the problem only exists for the version in stable. Given
| that an easy workaround exists, it's no big deal. Keeping this bug report
| around as documentation is probably sufficient.

I don't think it is applicable. Plain Debian stable systems still work (as
far as I know), and hence you only showed that it is possible to hose ones
system. That is, unless I am missing something here, simply a user error and
nothing we need to keep in the BTS.

Amicalement,  Dirk

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison

--- End Message ---