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commit d37de23ce6f51c6704e841e39209b6907ab4a78a Author: Andreas Tille <[email protected]> Date: Thu Oct 26 14:15:13 2017 +0200 Convert test scripts from ksh to sh --- debian/patches/ksh2sh.patch | 1085 +++++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 1086 insertions(+) diff --git a/debian/patches/ksh2sh.patch b/debian/patches/ksh2sh.patch new file mode 100644 index 0000000..d7ef11c --- /dev/null +++ b/debian/patches/ksh2sh.patch @@ -0,0 +1,1085 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Thu, 19 Oct 2017 16:27:56 +0200 +Description: Konvert test scripts from ksh to POSIX sh + +--- a/test/scripts/automated/belvu/test1 ++++ b/test/scripts/automated/belvu/test1 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test saving a file to MSF format +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o MSF $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If thre were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test10 ++++ b/test/scripts/automated/belvu/test10 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test the 'Print UPGMA-based subfamilies at cutoff' +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -X 0.5 $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test11 ++++ b/test/scripts/automated/belvu/test11 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test the 'Print UPGMA-based subfamilies at cutoff' +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -X 0.5 $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test12 ++++ b/test/scripts/automated/belvu/test12 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Create the tree using the UPGMA method and save it +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T u -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test13 ++++ b/test/scripts/automated/belvu/test13 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Create the tree using the UPGMA method and save it +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T u -o tree $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test14 ++++ b/test/scripts/automated/belvu/test14 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Create the tree using the Jukes-Cantor distance +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T j -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test15 ++++ b/test/scripts/automated/belvu/test15 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Create the tree using the Kimura distance +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T k -o tree $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test16 ++++ b/test/scripts/automated/belvu/test16 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Create the tree using the Kimura distance +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T k -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test17 ++++ b/test/scripts/automated/belvu/test17 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Create the tree using the Storm and Sonnhammer distance +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T s -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test18 ++++ b/test/scripts/automated/belvu/test18 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Create the tree using uncorrected distances and save +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T r -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test19 ++++ b/test/scripts/automated/belvu/test19 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Print the distance matrix +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -p $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test2 ++++ b/test/scripts/automated/belvu/test2 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test saving a file to Mul format +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Mul $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If thre were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test20 ++++ b/test/scripts/automated/belvu/test20 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Make the alignment non-redundanct and save +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -n 80 -o Mul $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test21 ++++ b/test/scripts/automated/belvu/test21 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Remove gappy columns and save the alignment +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -Q 60 -o MSF $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test22 ++++ b/test/scripts/automated/belvu/test22 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Remove gappy sequences and save the alignment in +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -q 80 -o Selex $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test23 ++++ b/test/scripts/automated/belvu/test23 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Ignore gaps in conservation calculation and print +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -i -c $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test24 ++++ b/test/scripts/automated/belvu/test24 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Remove partial sequences and save in aligned-fasta format +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -P -o FastaAlign $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test25 ++++ b/test/scripts/automated/belvu/test25 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Tests saving alignment without coordinates in Mul +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -C -o Mul $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test26 ++++ b/test/scripts/automated/belvu/test26 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Read in an alignment that has a separator of '=' +@@ -19,7 +19,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -z '=' -C -o MSF $data_dir/PF02171_seed_separator.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test27 ++++ b/test/scripts/automated/belvu/test27 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Read in an alignment that has a separator of '=' +@@ -19,7 +19,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -z '=' -R -C -o MSF $data_dir/PF02171_seed_separator.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test28 ++++ b/test/scripts/automated/belvu/test28 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Output random model probabilities for HMMER +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -p $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test29 ++++ b/test/scripts/automated/belvu/test29 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Output random model probabilities for HMMER +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -p $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test3 ++++ b/test/scripts/automated/belvu/test3 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test saving an alignment as Selex format +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test30 ++++ b/test/scripts/automated/belvu/test30 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Output random model probabilities for HMMER +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -p $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test31 ++++ b/test/scripts/automated/belvu/test31 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort alphabetically on start up. Also tests saving +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Fasta -S a -C $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test32 ++++ b/test/scripts/automated/belvu/test32 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by organism on start up. Also tests saving +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o FastaAlign -S o -C $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test33 ++++ b/test/scripts/automated/belvu/test33 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + + # Description: +@@ -17,7 +17,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S s -C -s $data_dir/PF02171_seed.scores $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test34 ++++ b/test/scripts/automated/belvu/test34 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + + # Description: +@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S n -s $data_dir/PF02171_seed.scores $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test35 ++++ b/test/scripts/automated/belvu/test35 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by neighbour-joinging tree on start up (large alignment). +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S n $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test36 ++++ b/test/scripts/automated/belvu/test36 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by neighbour-joinging tree on start up (large alignment). +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S n $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test37 ++++ b/test/scripts/automated/belvu/test37 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by UPGMA tree on start up (large alignment). +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S u $data_dir/PF02171_full.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test38 ++++ b/test/scripts/automated/belvu/test38 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by UPGMA tree on start up (large alignment). +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S u $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test39 ++++ b/test/scripts/automated/belvu/test39 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by similarity to first sequence (large alignment). +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S S $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test4 ++++ b/test/scripts/automated/belvu/test4 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test saving an alignment in aligned-fasta format +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o FastaAlign $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test40 ++++ b/test/scripts/automated/belvu/test40 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by similarity to first sequence +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S S $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test41 ++++ b/test/scripts/automated/belvu/test41 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a neighbour-joining tree (scoredist distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T nb -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test42 ++++ b/test/scripts/automated/belvu/test42 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a neighbour-joining tree (jukes-cantor distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T nj -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test43 ++++ b/test/scripts/automated/belvu/test43 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a neighbour-joining tree (kimura distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T nk -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test44 ++++ b/test/scripts/automated/belvu/test44 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a neighbour-joining tree (storm & sonnhammer distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T ns -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test45 ++++ b/test/scripts/automated/belvu/test45 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a neighbour-joining tree (uncorrected distances) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T nr -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test46 ++++ b/test/scripts/automated/belvu/test46 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a UPGMA tree (scoredist distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T ub -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test47 ++++ b/test/scripts/automated/belvu/test47 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a UPGMA tree (jukes-cantor distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T uj -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test48 ++++ b/test/scripts/automated/belvu/test48 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a UPGMA tree (kimura distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T uk -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test49 ++++ b/test/scripts/automated/belvu/test49 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a UPGMA tree (storm & sonnhammer distance correction) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T us -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test5 ++++ b/test/scripts/automated/belvu/test5 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test saving an alignment in unaligned-fasta format +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Fasta $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test50 ++++ b/test/scripts/automated/belvu/test50 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test creating a UPGMA tree (uncorrected distances) +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -T ur -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test51 ++++ b/test/scripts/automated/belvu/test51 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Sort by ID to first sequence +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o Selex -S i $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test6 ++++ b/test/scripts/automated/belvu/test6 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test saving a tree in new-hampshire format +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o tree $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test7 ++++ b/test/scripts/automated/belvu/test7 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test the option to print the conservation table +@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -c $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test8 ++++ b/test/scripts/automated/belvu/test8 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test the option to print the conservation table +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -c $data_dir/ALIGN.selex >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/belvu/test9 ++++ b/test/scripts/automated/belvu/test9 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test reading a file in 'raw' format. Check that it can +@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res + diffs=`belvu -o MSF -r $data_dir/PF02171_seed.fasta >&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/blixem/test1 ++++ b/test/scripts/automated/blixem/test1 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Blixem's --help option +@@ -18,7 +18,7 @@ results_file="$test_dir/$test_name""_res + diffs=`blixem -h 2>&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + RC=1 + fi +--- a/test/scripts/automated/blixem/test2 ++++ b/test/scripts/automated/blixem/test2 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Blixem's usage text +@@ -18,7 +18,7 @@ results_file="$test_dir/$test_name""_res + diffs=`blixem 2>&1 | diff "$results_file" -` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + RC=1 + fi +--- a/test/scripts/automated/dotter/test1 ++++ b/test/scripts/automated/dotter/test1 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # + # Description: +@@ -21,7 +21,7 @@ dotter -b $output_file -q 246634 -f $dat + diffs=`diff $results_file $output_file` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/dotter/test2 ++++ b/test/scripts/automated/dotter/test2 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # + # Description: +@@ -21,7 +21,7 @@ dotter -e $output_file -q 246634 -f $dat + diffs=`diff $results_file $output_file` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + print "$test_name FAILED" + RC=1 +--- a/test/scripts/automated/dotter/test3 ++++ b/test/scripts/automated/dotter/test3 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # + # Description: +@@ -24,7 +24,7 @@ dotter -b $output_file1 -e $output_file2 + diffs=`diff $results_file1 $output_file1` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + RC=1 + fi +@@ -33,7 +33,7 @@ fi + diffs=`diff $results_file2 $output_file2` + + # If there were any problems or differences, set RC +-if [[ $? -ne 0 || $diffs != "" ]] ++if [ $? -ne 0 -o "$diffs" != "" ] + then + RC=1 + fi +--- a/test/scripts/manual/belvu/test1 ++++ b/test/scripts/manual/belvu/test1 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test that the residue colors and markup colors are loaded correctly +--- a/test/scripts/manual/belvu/test2 ++++ b/test/scripts/manual/belvu/test2 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test that the residue colors and markup colors are loaded correctly +--- a/test/scripts/manual/belvu/test3 ++++ b/test/scripts/manual/belvu/test3 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test reading a file without stripping coordinates +--- a/test/scripts/manual/belvu/test4 ++++ b/test/scripts/manual/belvu/test4 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # Description: + # Test loading of match segments from a separate file + # +--- a/test/scripts/manual/belvu/test5 ++++ b/test/scripts/manual/belvu/test5 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test loading of match segments from a match-footer section +--- a/test/scripts/manual/blixem/test1 ++++ b/test/scripts/manual/blixem/test1 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Blixem in nucleotide mode. Features include nucleotide matches, transcripts +--- a/test/scripts/manual/blixem/test2 ++++ b/test/scripts/manual/blixem/test2 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Blixem in protein mode. Features include protein matches, transcripts +--- a/test/scripts/manual/dotter/test1 ++++ b/test/scripts/manual/dotter/test1 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Dotter in nucleotide->nucleotide mode. Tests the dot-matrix calculation as well +--- a/test/scripts/manual/dotter/test2 ++++ b/test/scripts/manual/dotter/test2 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Tests calling Dotter on a long sequence versus itself. Transcripts are supplied via a features +--- a/test/scripts/manual/dotter/test3 ++++ b/test/scripts/manual/dotter/test3 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Dotter in nucleotide->protein mode. Tests the dot-matrix calculation as well +--- a/test/scripts/manual/dotter/test4 ++++ b/test/scripts/manual/dotter/test4 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Dotter in nucleotide->protein mode, using the reverse-complemented version of the +--- a/test/scripts/manual/dotter/test5 ++++ b/test/scripts/manual/dotter/test5 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Dotter in nucleotide->nucleotide mode, using the reverse-complemented version of the input +--- a/test/scripts/manual/dotter/test6 ++++ b/test/scripts/manual/dotter/test6 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test Dotter in protein->protein mode. +--- a/test/scripts/manual/dotter/test7 ++++ b/test/scripts/manual/dotter/test7 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Test loading of a saved dot-matrix. +--- a/test/scripts/manual/dotter/test8 ++++ b/test/scripts/manual/dotter/test8 +@@ -1,4 +1,4 @@ +-#!/bin/ksh ++#!/bin/sh + # + # Description: + # Tests loading a dot-matrix plot from file for a long sequence versus itself. diff --git a/debian/patches/series b/debian/patches/series index 32c6ab5..af6d798 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -3,3 +3,4 @@ prevent_usage_of_blatsrc.patch use_debian_packaged_jsoncpp.patch fix_missing_includes.patch spelling.patch +ksh2sh.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
