Bug#693373: fsl-5.0: FSL randomise_parallel has a bashism that causes the defragmentation step to fail under dash

2012-11-19 Thread Michael Hanke 
reopen -1
reassign -1 fsl-4.1 4.1.9-7
retitle -1 fsl: FSL randomise_parallel has a bashism that causes the 
defragmentation step to fail under dash
thanks

Hi,

On Mon, Nov 19, 2012 at 10:55:45AM +0100, Gergely Nagy wrote:
> There's no fsl-5.0 package in Debian proper, please report this bug to
> the maintainers at t...@neuro.debian.net directly next time. (See
> http://neuro.debian.net/pkgs/fsl.html#neurodebian)
> 
> Since the package is not in Debian, I'm closing this report; maintainers
> are CC'd, though.

Thanks for CC'ing us Gergely. I should have responded earlier. This bug
may have been filed against a version that has not been uploaded yet,
however the bug is present in Debian proper as well. I'm trying to tag the
report properly now.

Michael


-- 
Michael Hanke
http://mih.voxindeserto.de


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Bug#693373: fsl-5.0: FSL randomise_parallel has a bashism that causes the defragmentation step to fail under dash

2012-11-15 Thread Philip Chase 
Package: fsl-5.0
Version: 5.0.0-1~nd60+1
Severity: normal

I found a bug in randomise_parallel that causes the defragmentation step to
fail at the end of the randomise run.  The error  log of the defragment job
shows

./GM_mod_merg_s3.defragment: 15: Bad substitution
./GM_mod_merg_s3.defragment: 15: Bad substitution
...
./GM_mod_merg_s3.defragment: 15: Bad substitution

If the shell is changed from dash to bash the defragment jobs works fine.  This
patch does the trick:

diff --git a/randomise_parallel b/randomise_parallel
index dc112c9..589033c 100755
--- a/randomise_parallel
+++ b/randomise_parallel
@@ -128,7 +128,7 @@ GENERATE_ID=`$FSLDIR/bin/fsl_sub -T ${REQUESTED_TIME} -N
${BASENAME}.generate -l

 #stage2:
 cat < ${DIRNAME}/${BASENAME}.defragment
-#!/bin/sh
+#!/bin/bash
 echo "Merging stat images"
 for FIRSTSEED in ${ROOTNAME}_SEED1_*_p_*.nii.gz
${ROOTNAME}_SEED1_*_corrp_*.nii.gz ; do
   ADDCOMMAND=""



-- System Information:
Debian Release: 6.0.5
  APT prefers stable
  APT policy: (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 2.6.32-5-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US, LC_CTYPE=en_US (charmap=ISO-8859-1)
Shell: /bin/sh linked to /bin/dash

Versions of packages fsl-5.0 depends on:
ii  bc  1.06.95-2The GNU bc arbitrary precision cal
ii  chromium-br 6.0.472.63~r59945-5+squeeze6 Chromium browser
ii  dc  1.06.95-2The GNU dc arbitrary precision rev
ii  epiphany-br 2.30.6-1 Intuitive GNOME web browser
ii  google-chro 23.0.1271.64-r165188 The web browser from Google
ii  iceweasel [ 3.5.16-17Web browser based on Firefox
ii  libc6   2.11.3-3 Embedded GNU C Library: Shared lib
ii  libexpat1   2.0.1-7+squeeze1 XML parsing C library - runtime li
ii  libgcc1 1:4.4.5-8GCC support library
ii  libgd2-noxp 2.0.36~rc1~dfsg-5GD Graphics Library version 2 (wit
ii  libgdchart- 0.11.5-7 Generate graphs using the GD libra
ii  libgiftiio0 1.0.9-1  IO library for the GIFTI cortical 
ii  libgl1-mesa 7.7.1-5  A free implementation of the OpenG
ii  libglu1-mes 7.7.1-5  The OpenGL utility library (GLU)
ii  libnewmat10 1.10.4-5 matrix manipulations library (C++)
ii  libnifti2   2.0.0-1  IO libraries for the NIfTI-1 data 
ii  libpng12-0  1.2.44-1+squeeze4PNG library - runtime
ii  libstdc++6  4.4.5-8  The GNU Standard C++ Library v3
ii  python  2.6.6-3+squeeze7 interactive high-level object-orie
ii  tcl8.4  8.4.19-4 Tcl (the Tool Command Language) v8
ii  tcsh [c-she 6.17.02-4TENEX C Shell, an enhanced version
ii  tk8.4   8.4.19-4 Tk toolkit for Tcl and X11, v8.4 -
ii  w3m [www-br 0.5.2-9  WWW browsable pager with excellent
ii  zlib1g  1:1.2.3.4.dfsg-3 compression library - runtime

Versions of packages fsl-5.0 recommends:
ii  fsl-atlases 5.0.0-2  FSL's MNI152 standard space stereo
ii  fsl-doc-5.0 5.0.0-1~nd60+1   documentation for FSL
ii  fslview 3.1.8+4.1.9-1~nd60+1 viewer for (f)MRI and DTI data

Versions of packages fsl-5.0 suggests:
ii  dicomnifti   2.30.0-1~nd60+1 converts DICOM files into the NIfT
ii  fsl-feeds5.0.0-1 FSL Evaluation and Example Data Su
ii  fsl-first-data   5.0.0-2 model data for FIRST subcortical b
ii  fsl-possum-data  5.0.0-2 sequence templates for the POSSUM 
pn  gridengine-client  (no description available)
pn  octave | octave3.2 (no description available)

-- no debconf information


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