Your message dated Thu, 17 Jul 2014 19:33:36 +0000 with message-id <[email protected]> and subject line Bug#693373: fixed in fsl 5.0.7-2 has caused the Debian Bug report #693373, regarding fsl: 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 ---Source: fsl Source-Version: 5.0.7-2 We believe that the bug you reported is fixed in the latest version of fsl, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael Hanke <[email protected]> (supplier of updated fsl package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 1.8 Date: Thu, 17 Jul 2014 15:44:44 +0200 Source: fsl Binary: fsl fsl-5.0 fsl-core fsl-5.0-core Architecture: source amd64 all Version: 5.0.7-2 Distribution: unstable Urgency: low Maintainer: NeuroDebian Team <[email protected]> Changed-By: Michael Hanke <[email protected]> Description: fsl - transitional dummy package fsl-5.0 - transitional dummy package fsl-5.0-core - analysis tools for FMRI, MRI and DTI brain imaging fsl-core - metapackage for the latest version of FSL Closes: 685757 693373 695257 Changes: fsl (5.0.7-2) unstable; urgency=low . * Add a patch to make randomise_parallel work on systems that do not have bash as their default shell (Closes: #693373). Thanks to Philip Chase for the patch. * Add a patch to honor an unset FSLPARALLEL (do not submit jobs to a cluster) even in cases where SGE_ROOT is set (Closes: #685757). Thanks to German Gomez-Herrero for the patch. * Sanitize PATH and LD_LIBRARY_PATH when sourcing the configuration file. Old/duplicate FSL path entries are now removed (Closes: #695257). Thanks to Vincent Kersten for the patch. Checksums-Sha1: fdd30310a8f7f4d7a4c934f7c04fa2e98b3f786b 2496 fsl_5.0.7-2.dsc d590beb5738304d60da422bf9c39341765e35930 36000 fsl_5.0.7-2.debian.tar.xz 68cc2cff8d7b4a57c21af8b84edf86b76f3cd11c 8309864 fsl-5.0-core_5.0.7-2_amd64.deb efff40ce119b5edb30b5d8c9c2e679ce21e24882 20070 fsl_5.0.7-2_all.deb d116eb82f0a753cd4dd5ed511dd50e3accfbd6af 18658 fsl-5.0_5.0.7-2_all.deb c79e937c667021a98456e55e3fdbc4bbb50f2ffd 19930 fsl-core_5.0.7-2_all.deb Checksums-Sha256: db2afe3fd6d98709f589c5b536400e74c7aba8575d291b213dae1eb602458948 2496 fsl_5.0.7-2.dsc cca299a22345ab34692c47cef1ac234c82f886fe67420d05f507b0582128630b 36000 fsl_5.0.7-2.debian.tar.xz b346b42af27c139e7607b21704a834d837b49c7d9400cbe69ad93fa13222a787 8309864 fsl-5.0-core_5.0.7-2_amd64.deb 04d7dbf22acdcf7ca9d92d89ba895577112c235e605412f89c48c9a22a1a71ba 20070 fsl_5.0.7-2_all.deb 2eb4bb6f093bb593f8f2548ce5996775184f2039b7be7bdd3344aa5dcc72b2af 18658 fsl-5.0_5.0.7-2_all.deb 4daab31e793b02a415f823e6626a6b0ad8421095a2c9cebdf700b502a714c29a 19930 fsl-core_5.0.7-2_all.deb Files: 8dc304e509ea68c84b3dcb4a94f53346 8309864 non-free/science optional fsl-5.0-core_5.0.7-2_amd64.deb ea96cc7041d15c7e0dd2ce7db5a19c0b 20070 non-free/oldlibs optional fsl_5.0.7-2_all.deb 487eedd7c893a9a52ab8333f3803f84c 18658 non-free/oldlibs optional fsl-5.0_5.0.7-2_all.deb 7f9b39961292d97e5b090f9862ab4837 19930 non-free/science optional fsl-core_5.0.7-2_all.deb a962ffbe6fae329043cf51ea592995ea 2496 non-free/science optional fsl_5.0.7-2.dsc cb60efc98a2d5153d3b5cf15943eb7a8 36000 non-free/science optional fsl_5.0.7-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBAgAGBQJTyCCTAAoJEMBz0ih/+56bYnsP/jtH7zBNtagGn5/YOGFfEX5V z/L0s2qZ6ELoTWg9lD1qsxQN3HjBJLmJgsZDNhgCtIrZSYkZSPif58D0bGGsJVRj 863bk5hrp5diITQIarmGWDFHaXBR8phuOafBd0OZ7WYbtXYkkSKkBD12p/3Z2Crd g3kKlGaBngKCsfhF//CcdOJHQbryR//VpU/a5DwWxhcoxhJBZrxIzfq6RlKdbaLN Gpg1igpA4mz0V52gHOYBtous+slVx2n7kqo0hv/vTgZ7CVqq1sNhu7AGNYxcXPTV aSCPKYdF5jJUV6bJt+KJulsREEUaiBxhbbHqek7QwE3/UZzv6pvI4BMkgeZJR2xn i7PP2LpsGWvGzqVnFt15ZcRoJa+Oeae+Kikd8uAI1adnbAGLUfTkwiYR98EL6Xet RKya9U5XUxqOQjjvi4Nj3xGL50LyK1jOQ5QaNG6SbHS+KN/lYRohEu8qoQW0y4/E DQbB9/oMl7+Ez/p/pyXVegWOeHt7QHc6LUdc19L5fuSl4XraMpqMspf5kqaKFDSu St9xAokoOaztsLQo/zVx0zT9UFZxXAShH0fCxu1UyabigBeEBR5d1JtoMhEA3VK4 DYj3XC4lOGDetrTFAzuj5HdqwRePww0I4PwAvvetth5vKoaQGnUIPmXMNZC9A54m 7z1qOyIzVy4Oe4Xpz8M6 =ra/6 -----END PGP SIGNATURE-----
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