Library dependency error in littler-0.1.0-1

[Andy Dustman]

Binary package hint: littler

I have littler and r-base and their dependencies installed. r (from littler) can't start because it can't find libRblas.so:

$ ldd /usr/bin/r
 linux-vdso.so.1 => (0x00007fffba5fe000)
 libR.so => /usr/lib/R/lib/libR.so (0x00007ffdb1d0c000)
 libRblas.so => not found
 libRlapack.so => /usr/lib/R/lib/libRlapack.so (0x00007ffdb191e000)
 libc.so.6 => /lib/libc.so.6 (0x00007ffdb15bc000)
 libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007ffdb1342000)
 libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0x00007ffdb1083000)
 libm.so.6 => /lib/libm.so.6 (0x00007ffdb0e02000)
 libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007ffdb0bf4000)
 libreadline.so.5 => /lib/libreadline.so.5 (0x00007ffdb09b4000)
 libpcre.so.3 => /usr/lib/libpcre.so.3 (0x00007ffdb078e000)
 libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007ffdb057e000)
 libz.so.1 => /usr/lib/libz.so.1 (0x00007ffdb0367000)
 libdl.so.2 => /lib/libdl.so.2 (0x00007ffdb0163000)
 /lib64/ld-linux-x86-64.so.2 (0x00007ffdb2217000)
 libncurses.so.5 => /lib/libncurses.so.5 (0x00007ffdaff28000)

R itself does not link against libRblas.so:

$ ldd /usr/lib/R/bin/exec/R
 linux-vdso.so.1 => (0x00007fffc51fe000)
 libR.so => /usr/lib/R/lib/libR.so (0x00007fa9bca20000)
 libc.so.6 => /lib/libc.so.6 (0x00007fa9bc6be000)
 libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007fa9bc444000)
 libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0x00007fa9bc185000)
 libm.so.6 => /lib/libm.so.6 (0x00007fa9bbf04000)
 libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fa9bbcf6000)
 libreadline.so.5 => /lib/libreadline.so.5 (0x00007fa9bbab6000)
 libpcre.so.3 => /usr/lib/libpcre.so.3 (0x00007fa9bb890000)
 libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007fa9bb680000)
 libz.so.1 => /usr/lib/libz.so.1 (0x00007fa9bb469000)
 libdl.so.2 => /lib/libdl.so.2 (0x00007fa9bb265000)
 /lib64/ld-linux-x86-64.so.2 (0x00007fa9bcf2b000)
 libncurses.so.5 => /lib/libncurses.so.5 (0x00007fa9bb02a000)

Note that both do link against libblas.so.3gf. The R libraries (in /usr/lib/R/lib) only include libRlapack.so and libR.so.

My suspicion is that littler needs to be rebuilt against the updated R packaging.

Description: Ubuntu 8.04
Release: 8.04

littler:
  Installed: 0.1.0-1
  Candidate: 0.1.0-1
  Version table:
 *** 0.1.0-1 0
        500 http://us.archive.ubuntu.com hardy/universe Packages
        500 ftp://ftp.uga.edu hardy/universe Packages
        100 /var/lib/dpkg/status

r-base:
  Installed: 2.6.2-2
  Candidate: 2.6.2-2
  Version table:
 *** 2.6.2-2 0
        500 http://us.archive.ubuntu.com hardy/universe Packages
        500 ftp://ftp.uga.edu hardy/universe Packages
        100 /var/lib/dpkg/status

[Cesare Tirabassi (norsetto)]

>The R libraries (in /usr/lib/R/lib) only include libRlapack.so and libR.so

This is pretty strange as libRblas.so is provided by the r-base-core package (/usr/lib/R/lib/libRblas.so) which is a required dependency of littler (and r-base).
Note that r-base is just a meta package and in principle can be safely removed.

[Andy Dustman (farcepest)]

r-base-core-2.6.2-2 doesn't include libRblas.so though.

$ dpkg-query -L r-base-core | grep blas
$ # no output

r-base-core:
  Installed: 2.6.2-2
  Candidate: 2.6.2-2
  Version table:
 *** 2.6.2-2 0
        500 http://us.archive.ubuntu.com hardy/universe Packages
        500 ftp://ftp.uga.edu hardy/universe Packages
        100 /var/lib/dpkg/status

[Cesare Tirabassi (norsetto)]

motu-release subscribed to ack this upload.
littler needs to be rebuilt due to the new R package (gfortran transition).
debdiff is attached, package builds and installs ok.

[Cesare Tirabassi (norsetto)]

root@norsetto:/root/debian# apt-get install littler
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
  libblas3gf r-base-core
Suggested packages:
  ess r-base-html r-base-latex r-doc-info r-doc-pdf r-doc-html r-mathlib
Recommended packages:
  r-base-dev r-recommended
The following NEW packages will be installed:
  libblas3gf littler r-base-core
0 upgraded, 3 newly installed, 0 to remove and 29 not upgraded.
Need to get 10.8MB/10.8MB of archives.
After this operation, 34.2MB of additional disk space will be used.
Do you want to continue [Y/n]?
WARNING: The following packages cannot be authenticated!
  littler
Install these packages without verification [y/N]? y
Get:1 http://archive.ubuntu.com hardy/main libblas3gf 1.2-1.3ubuntu3 [221kB]
Get:2 http://archive.ubuntu.com hardy/universe r-base-core 2.6.2-2 [10.6MB]
Fetched 10.8MB in 1min33s (116kB/s)
Can not write log, openpty() failed (/dev/pts not mounted?)
Selecting previously deselected package libblas3gf.
(Reading database ... 294315 files and directories currently installed.)
Unpacking libblas3gf (from .../libblas3gf_1.2-1.3ubuntu3_amd64.deb) ...
Selecting previously deselected package r-base-core.
Unpacking r-base-core (from .../r-base-core_2.6.2-2_amd64.deb) ...
Selecting previously deselected package littler.
Unpacking littler (from .../littler_0.1.0-1ubuntu1_amd64.deb) ...
Can not write log, openpty() failed (/dev/pts not mounted?)
Setting up libblas3gf (1.2-1.3ubuntu3) ...

Setting up r-base-core (2.6.2-2) ...
Setting R_PAPERSIZE_USER default to 'a4'

Setting up littler (0.1.0-1ubuntu1) ...
Processing triggers for libc6 ...
ldconfig deferred processing now taking place
root@norsetto:/root/debian# ldd /usr/bin/r
        libR.so => /usr/lib64/R/lib/libR.so (0x00002affa8e27000)
        libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00002affa9346000)
        libRlapack.so => /usr/lib64/R/lib/libRlapack.so (0x00002affa95c0000)
        libc.so.6 => /lib/libc.so.6 (0x00002affa99ae000)
        libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0x00002affa9d11000)
        libm.so.6 => /lib/libm.so.6 (0x00002affa9fd0000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002affaa251000)
        libreadline.so.5 => /lib/libreadline.so.5 (0x00002affaa460000)
        libpcre.so.3 => /usr/lib/libpcre.so.3 (0x00002affaa6a0000)
        libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00002affaa8c6000)
        libz.so.1 => /usr/lib/libz.so.1 (0x00002affaaad7000)
        libdl.so.2 => /lib/libdl.so.2 (0x00002affaacee000)
        /lib64/ld-linux-x86-64.so.2 (0x00002affa8c08000)
        libncurses.so.5 => /lib/libncurses.so.5 (0x00002affaaef2000)

[Scott Kitterman (kitterman)]

Ack and I don't mind if you ack your own.

[Launchpad Janitor (janitor)]

This bug was fixed in the package littler - 0.1.0-1ubuntu1

---------------
littler (0.1.0-1ubuntu1) hardy; urgency=low

  * Rebuilt under R 2.6.2 (LP: #217742)
  * debian/control: Updated (Build-)Depends accordingly
  * Modify Maintainer value to match the DebianMaintainerField
    specification.

 -- Cesare Tirabassi <email address hidden> Tue, 15 Apr 2008 21:28:50 +0200