Your message dated Mon, 19 Nov 2012 10:55:45 +0100 with message-id <[email protected]> and subject line Re: Bug#693373: fsl-5.0: FSL randomise_parallel has a bashism that causes the defragmentation step to fail under dash has caused the Debian Bug report #693373, regarding fsl-5.0: FSL randomise_parallel has a bashism that causes the defragmentation step to fail under dash to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 693373: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=693373 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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 <<combineScript > ${DIRNAME}/${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 1.06.95-2 The GNU bc arbitrary precision cal ii chromium-br 6.0.472.63~r59945-5+squeeze6 Chromium browser ii dc 1.06.95-2 The 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 [ 3.5.16-17 Web 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 1:4.4.5-8 GCC support library ii libgd2-noxp 2.0.36~rc1~dfsg-5 GD 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+squeeze4 PNG 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 6.17.02-4 TENEX 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-feeds 5.0.0-1 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 <none> (no description available) pn octave | octave3.2 <none> (no description available) -- no debconf information
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--- Begin Message ---Philip Chase <[email protected]> writes: > Package: fsl-5.0 > Version: 5.0.0-1~nd60+1 There's no fsl-5.0 package in Debian proper, please report this bug to the maintainers at [email protected] 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. -- |8]
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