[med-svn] [Git][med-team/roguenarok][master] 7 commits: Remove d/tests/data since upstream vendors the same as example in source
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Thu Oct 7 16:32:03 BST 2021
Nilesh Patra pushed to branch master at Debian Med / roguenarok
Commits:
e9bf725a by Nilesh Patra at 2021-10-07T20:05:33+05:30
Remove d/tests/data since upstream vendors the same as example in source
- - - - -
d6e490d0 by Nilesh Patra at 2021-10-07T20:06:12+05:30
d/examples: Install examples/* instead
- - - - -
389cd835 by Nilesh Patra at 2021-10-07T20:17:55+05:30
d/p/hardening.patch: Append options to CFLAGS and pass hardening options properly to vendor dbg and fix blhc
- - - - -
82e3fca7 by Nilesh Patra at 2021-10-07T20:21:22+05:30
d/rules: s/make/$(MAKE)/g
- - - - -
b6756852 by Nilesh Patra at 2021-10-07T15:27:06+00:00
d/p/fix-manpage-call-and-help-exit-code.patch
* Help option path is called with a relative path in current dir, remove the relative dir
* Exits with abort() after printing help, exit with 0 instead
- - - - -
646f5a55 by Nilesh Patra at 2021-10-07T15:27:06+00:00
Update manpages
- - - - -
c5dba1bc by Nilesh Patra at 2021-10-07T20:59:16+05:30
Upload to unstable
- - - - -
14 changed files:
- debian/changelog
- debian/examples
- debian/mans/rnr-lsi.1
- debian/mans/rnr-mast.1
- debian/mans/rnr-prune.1
- debian/mans/rnr-tii.1
- debian/mans/roguenarok-parallel.1
- debian/mans/roguenarok-single.1
- + debian/patches/fix-manpage-call-and-help-exit-code.patch
- debian/patches/hardening.patch
- debian/patches/series
- debian/rules
- − debian/tests/data/150.bs
- − debian/tests/data/150.tre
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+roguenarok (1.0.1-2) unstable; urgency=medium
+
+ * Team Upload.
+ * Remove d/tests/data since upstream vendors the same as example in source
+ * d/examples: Install examples/* instead
+ * d/p/hardening.patch: Append options to CFLAGS and pass hardening
+ options properly to vendor dbg and fix blhc
+ * d/rules: s/make/$(MAKE)/g
+ * d/p/fix-manpage-call-and-help-exit-code.patch
+ + Help option path is called with a relative path in current
+ dir, remove the relative dir path in help display
+ + Exits with abort() after printing help, exit with 0 instead
+ * Update manpages
+
+ -- Nilesh Patra <nilesh at debian.org> Thu, 07 Oct 2021 20:22:14 +0530
+
roguenarok (1.0.1-1) unstable; urgency=medium
* Fix watchfile to detect new versions on github
=====================================
debian/examples
=====================================
@@ -1 +1 @@
-debian/tests/data/*
\ No newline at end of file
+example/*
=====================================
debian/mans/rnr-lsi.1
=====================================
@@ -1,26 +1,36 @@
-.TH RNR-LSI "1" "March 2017" "rnr-lsi 1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH RNR-LSI "1" "October 2021" "rnr-lsi 1.0.1" "User Commands"
.SH NAME
rnr-lsi \- computes three flavors of leaf stability index for each taxon
-.SH SYNOPSIS
-.B rnr\-lsi
-\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
-.SH OPTIONS
-.SS OBLIGATORY
-.TP
+.SH DESCRIPTION
+This is RnR\-lsi version 1.0.1 released by Andre J. Aberer in 2021\-06\-07.
+.PP
+This program computes three flavors of leaf stability index for each taxon.
+.PP
+SYNTAX: rnr\-lsi \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
+.IP
+OBLIGATORY:
+.PP
\fB\-i\fR <bootTrees>
+.IP
A collection of bootstrap trees.
-.TP
+.PP
\fB\-n\fR <runId>
+.IP
An identifier for this run.
-.SS OPTIONAL
-.TP
+.IP
+OPTIONAL:
+.PP
\fB\-x\fR <excludeFile>
+.IP
Prune the taxa in the file first (one taxon per line), before computing the lsi.
-.TP
+.PP
\fB\-w\fR <workDir>
+.IP
A working directory where output files are created.
-.TP
+.PP
\fB\-h\fR
+.IP
This help file.
.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/rnr-mast.1
=====================================
@@ -1,34 +1,45 @@
-.TH RNR-MAST "1" "March 2017" "rnr-mast 1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH RNR-MAST "1" "October 2021" "rnr-mast 1.0.1" "User Commands"
.SH NAME
rnr-mast \- computes maximum agreement trees for unrooted input sets
-.SH SYNOPSIS
-.B rnr\-mast
-\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-a] [\-x <excludeFile>]
-.SH OPTIONS
-.SS OBLIGATORY
-.TP
+.SH DESCRIPTION
+This is RnR\-mast version 1.0 released by Andre J. Aberer in 2011\-10\-25.
+.PP
+This program computes maximum agreement trees for unrooted input sets.
+.PP
+SYNTAX: rnr\-mast \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-a] [\-x <excludeFile>]
+.PP
+OBLIGATORY:
\fB\-i\fR <bootTrees>
+.IP
A collection of bootstrap trees.
-.TP
+.PP
\fB\-n\fR <runId>
+.IP
An identifier for this run.
-.SS OPTIONAL
-.TP
+.PP
+OPTIONAL
\fB\-a\fR
+.IP
Compute all possible MAST trees. Without this flag, you will
+.IP
only get a few MASTs that are easy to compute. As there may be an
exponential number of MASTs, use this option with care.
-.TP
+.PP
\fB\-w\fR <workDir>
+.IP
A working directory where output files are created.
-.TP
+.PP
\fB\-x\fR <excludeFile>
+.IP
Exclude the taxa in this file (one taxon per line)
+.IP
prior to computing the MAST. If you compute all MASTs anyway, this
option is option will not be useful. However, you can use this option
to speed up things.
-.TP
+.PP
\fB\-h\fR
+.IP
This help file.
.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/rnr-prune.1
=====================================
@@ -1,31 +1,40 @@
-.TH RNR-PRUNE "1" "March 2017" "rnr-prune 1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH RNR-PRUNE "1" "October 2021" "rnr-prune 1.0.1" "User Commands"
.SH NAME
rnr-prune \- prunes a list of taxa from a bootstrap tree or a single tree with branch lengths
-.SH SYNOPSIS
-.B rnr\-prune
-[\-i <bootTrees> | \fB\-t\fR <treeFile>] \fB\-x\fR <excludeFile> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
.SH DESCRIPTION
+This is RnR\-prune version 1.0 released by Andre J. Aberer in 2011\-10\-25.
+.PP
This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best\-known ML/MP\-tree).
-.SH OPTIONS
-.SS OBLIGATORY
-.TP
+.PP
+SYNTAX: rnr\-prune [\-i <bootTrees> | \fB\-t\fR <treeFile>] \fB\-x\fR <excludeFile> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
+.IP
+OBLIGATORY:
+.PP
\fB\-x\fR <excludeFile>
+.IP
A list of taxa (one taxon per line) to prune from either the bootstrap trees or the single best\-known tree.
-.TP
+.PP
\fB\-i\fR <bootTrees>
+.IP
A collection of bootstrap trees.
-.TP
+.PP
\fB\-t\fR <treeFile>
+.IP
A single tree with branch lengths. Use either this flag or the \fB\-i\fR flag.
-.TP
+.PP
\fB\-n\fR <runId>
+.IP
An identifier for this run.
-.SS OPTIONAL
-.TP
+.IP
+OPTIONAL:
+.PP
\fB\-w\fR <workDir>
+.IP
A working directory where output files are created.
-.TP
+.PP
\fB\-h\fR
+.IP
This help file.
.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/rnr-tii.1
=====================================
@@ -1,29 +1,38 @@
-.TH RNR-TII "1" "March 2017" "rnr-tii 1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH RNR-TII "1" "October 2021" "rnr-tii 1.0.1" "User Commands"
.SH NAME
rnr-tii \- computes the taxonomic instability index
-.SH SYNOPSIS
-.B rnr\-tii
-\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-x <excludeFile>]
-.SH OPTIONS
-.SS OBLIGATORY
-.TP
+.SH DESCRIPTION
+This is RnR\-tii version 1.0 released by Andre J. Aberer in 2011\-10\-25..
+.PP
+This program computes the taxonomic instability index.
+.PP
+SYNTAX: rnr\-tii \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-x <excludeFile>]
+.PP
+OBLIGATORY:
\fB\-i\fR <bootTrees>
+.IP
A collection of bootstrap trees.
-.TP
+.PP
\fB\-n\fR <runId>
+.IP
An identifier for this run.
-.SS OPTIONAL
-.TP
+.PP
+OPTIONAL
\fB\-z\fR <z>
+.IP
The exponent used in the TII formula. Use small values to emphasize close relationships and vice versa. DEFAULT: 2
-.TP
+.PP
\fB\-w\fR <workDir>
+.IP
A working directory where output files are created.
-.TP
+.PP
\fB\-x\fR <excludeFile>
+.IP
Exclude the taxa in this file (one taxon per line) prior to computing the TII.
-.TP
+.PP
\fB\-h\fR
+.IP
This help file.
.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/roguenarok-parallel.1
=====================================
@@ -1,65 +1,82 @@
-.TH ROGUENAROK-PARALLEL "1" "March 2017" "roguenarok-parallel 1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH ROGUENAROK-PARALLEL "1" "October 2021" "roguenarok-parallel 1.0.1" "User Commands"
.SH NAME
roguenarok-parallel \- implements the RogueNaRok algorithm for rogue taxon identification (parallel version)
-.SH SYNOPSIS
-.B roguenarok-parallel
-\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
-.SH OPTIONS
-.SS OBLIGATORY
-.TP
+.SH DESCRIPTION
+roguenarok\-parallel: invalid option \fB\-\-\fR '\-'
+.PP
+This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011\-10\-25.
+.PP
+This program implements the RogueNaRok algorithm for rogue taxon identification.
+.PP
+SYNTAX: RogueNaRok \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
+.IP
+OBLIGATORY:
+.PP
\fB\-i\fR <bootTrees>
+.IP
A collection of bootstrap trees.
-.TP
+.PP
\fB\-n\fR <runId>
+.IP
An identifier for this run.
-.TP
-\fB\-T\fR <num>
-Execute RogueNaRok in parallel with <num> threads.
-.SS OPTIONAL
-.TP
+.IP
+OPTIONAL:
+.PP
\fB\-t\fR <bestKnownTree>
+.IP
If a single best\-known tree (such as an ML or MP
tree) is provided, RogueNaRok optimizes the bootstrap support in this
best\-known tree (still drawn from the bootstrap trees). The threshold
parameter is ignored.
-.TP
+.PP
\fB\-x\fR <excludeFile>
+.IP
taxa in this file (one taxon per line) will not be
considered for pruning.
-.TP
+.PP
\fB\-c\fR <threshold>
+.IP
A threshold or mode for the consensus tree that is
+.IP
optimized. Specify a value between 50 (majority rule consensus) and
100 (strict consensus) or MR (for the extended majority rule
consensus). Note that rogue taxa identified with respect to different
thresholds can vary substantially. DEFAULT: MR consensus
-.TP
+.PP
\fB\-b\fR
+.IP
Instead of trying to maximize the support in the consensus tree,
the RogueNaRok will try to maximize the number of bipartition in the
final tree by pruning taxa. DEFAULT: off
-.TP
+.PP
\fB\-L\fR <factor>
+.IP
a weight factor to penalize for dropset size.
Factor=1 is Pattengale's criterion. The higher the value, the more
conservative the algorithm is in pruning taxa. DEFAULT: 0.0 (=RBIC)
-.TP
+.PP
\fB\-s\fR <dropsetSize>
+.IP
maximum size of dropset per iteration. If
dropsetSize == n, then RogueNaRok will test in each iteration which
tuple of n taxa increases optimality criterion the most and prunes
taxa accordingly. This improves the result, but runtimes will
increase at least linearly. DEFAULT: 1
-.TP
+.PP
\fB\-w\fR <workDir>
+.IP
A working directory where output files are created.
-.TP
+.PP
+\fB\-T\fR <num>
+.IP
+Execute RogueNaRok in parallel with <num> threads. You need to compile the program for parallel execution first.
+.PP
\fB\-h\fR
-This help file.
-.SH EXAMPLES
.IP
-roguenarok-parallel -T2 \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
+This help file.
+.PP
+MINIMAL EXAMPLE:
+\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
.SH AUTHOR
-RogueNaRok was released by Andre J. Aberer in 2011\-10\-25.
-.P
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/roguenarok-single.1
=====================================
@@ -1,62 +1,82 @@
-.TH ROGUENAROK-SINGLE "1" "March 2017" "roguenarok-single 1.0" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH ROGUENAROK-SINGLE "1" "October 2021" "roguenarok-single 1.0.1" "User Commands"
.SH NAME
roguenarok-single \- implements the RogueNaRok algorithm for rogue taxon identification (single core version)
-.SH SYNOPSIS
-.B roguenarok-single
-\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
-.SH OPTIONS
-.SS OBLIGATORY
-.TP
+.SH DESCRIPTION
+ERROR: Please specify a file containing bootstrap trees via \fB\-i\fR.
+.PP
+This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011\-10\-25.
+.PP
+This program implements the RogueNaRok algorithm for rogue taxon identification.
+.PP
+SYNTAX: RogueNaRok \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
+.IP
+OBLIGATORY:
+.PP
\fB\-i\fR <bootTrees>
+.IP
A collection of bootstrap trees.
-.TP
+.PP
\fB\-n\fR <runId>
+.IP
An identifier for this run.
-.SS OPTIONAL
-.TP
+.IP
+OPTIONAL:
+.PP
\fB\-t\fR <bestKnownTree>
+.IP
If a single best\-known tree (such as an ML or MP
tree) is provided, RogueNaRok optimizes the bootstrap support in this
best\-known tree (still drawn from the bootstrap trees). The threshold
parameter is ignored.
-.TP
+.PP
\fB\-x\fR <excludeFile>
+.IP
taxa in this file (one taxon per line) will not be
considered for pruning.
-.TP
+.PP
\fB\-c\fR <threshold>
+.IP
A threshold or mode for the consensus tree that is
+.IP
optimized. Specify a value between 50 (majority rule consensus) and
100 (strict consensus) or MR (for the extended majority rule
consensus). Note that rogue taxa identified with respect to different
thresholds can vary substantially. DEFAULT: MR consensus
-.TP
+.PP
\fB\-b\fR
+.IP
Instead of trying to maximize the support in the consensus tree,
the RogueNaRok will try to maximize the number of bipartition in the
final tree by pruning taxa. DEFAULT: off
-.TP
+.PP
\fB\-L\fR <factor>
+.IP
a weight factor to penalize for dropset size.
Factor=1 is Pattengale's criterion. The higher the value, the more
conservative the algorithm is in pruning taxa. DEFAULT: 0.0 (=RBIC)
-.TP
+.PP
\fB\-s\fR <dropsetSize>
+.IP
maximum size of dropset per iteration. If
dropsetSize == n, then RogueNaRok will test in each iteration which
tuple of n taxa increases optimality criterion the most and prunes
taxa accordingly. This improves the result, but runtimes will
increase at least linearly. DEFAULT: 1
-.TP
+.PP
\fB\-w\fR <workDir>
+.IP
A working directory where output files are created.
-.TP
+.PP
+\fB\-T\fR <num>
+.IP
+Execute RogueNaRok in parallel with <num> threads. You need to compile the program for parallel execution first.
+.PP
\fB\-h\fR
-This help file.
-.SH EXAMPLES
.IP
-roguenarok-single \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
+This help file.
+.PP
+MINIMAL EXAMPLE:
+\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
.SH AUTHOR
-RogueNaRok was released by Andre J. Aberer in 2011\-10\-25.
-.P
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/patches/fix-manpage-call-and-help-exit-code.patch
=====================================
@@ -0,0 +1,105 @@
+Description: This does two things
+ * Help option path is called with a relative path in current dir, remove the relative dir
+ * Exits with abort() after printing help, exit with 0 instead
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-10-07
+--- a/RogueNaRok.c
++++ b/RogueNaRok.c
+@@ -2107,7 +2107,7 @@
+ void printHelpFile()
+ {
+ printVersionInfo(FALSE);
+- printf("This program implements the RogueNaRok algorithm for rogue taxon identification.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-x <excludeFile>] [-c <threshold>] [-b] [-s <dropsetSize>] [-w <workingDir>] [-h]\n", programName);
++ printf("This program implements the RogueNaRok algorithm for rogue taxon identification.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-x <excludeFile>] [-c <threshold>] [-b] [-s <dropsetSize>] [-w <workingDir>] [-h]\n", programName);
+ printf("\n\tOBLIGATORY:\n");
+ printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");
+ printf("-n <runId>\n\tAn identifier for this run.\n");
+@@ -2219,7 +2219,7 @@
+ default:
+ {
+ printHelpFile();
+- abort ();
++ exit(0);
+ }
+ }
+
+--- a/rnr-lsi.c
++++ b/rnr-lsi.c
+@@ -327,7 +327,7 @@
+ void printHelpFile()
+ {
+ printVersionInfo(FALSE);
+- printf("This program computes three flavors of leaf stability index for each taxon.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));
++ printf("This program computes three flavors of leaf stability index for each taxon.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));
+ printf("\n\tOBLIGATORY:\n");
+ printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");
+ printf("-n <runId>\n\tAn identifier for this run.\n");
+@@ -372,7 +372,7 @@
+ default:
+ {
+ printHelpFile();
+- abort ();
++ exit(0);
+ }
+ }
+ }
+--- a/rnr-mast.c
++++ b/rnr-mast.c
+@@ -873,7 +873,7 @@
+ void printHelpFile()
+ {
+ printVersionInfo(FALSE);
+- printf("This program computes maximum agreement trees for unrooted input sets.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-a] [-x <excludeFile>]\n", lowerTheString(programName));
++ printf("This program computes maximum agreement trees for unrooted input sets.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-a] [-x <excludeFile>]\n", lowerTheString(programName));
+ printf("\nOBLIGATORY:\n");
+ printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");
+ printf("-n <runId>\n\tAn identifier for this run.\n");
+@@ -929,7 +929,7 @@
+ default:
+ {
+ printHelpFile();
+- abort ();
++ exit(0);
+ }
+ }
+ }
+--- a/rnr-prune.c
++++ b/rnr-prune.c
+@@ -140,7 +140,7 @@
+ static void printHelpFile()
+ {
+ printVersionInfo(FALSE);
+- printf("This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best-known ML/MP-tree).\n\nSYNTAX: ./%s [-i <bootTrees> | -t <treeFile>] -x <excludeFile> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));
++ printf("This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best-known ML/MP-tree).\n\nSYNTAX: %s [-i <bootTrees> | -t <treeFile>] -x <excludeFile> -n <runId> [-w <workingDir>] [-h]\n", lowerTheString(programName));
+ printf("\n\tOBLIGATORY:\n");
+ printf("-x <excludeFile>\n\tA list of taxa (one taxon per line) to prune from either the bootstrap trees or the single best-known tree.\n");
+ printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");
+@@ -189,7 +189,7 @@
+ default:
+ {
+ printHelpFile();
+- abort();
++ exit(0);
+ }
+ }
+ }
+--- a/rnr-tii.c
++++ b/rnr-tii.c
+@@ -245,7 +245,7 @@
+ void printHelpFile()
+ {
+ printVersionInfo(FALSE);
+- printf("This program computes the taxonomic instability index.\n\nSYNTAX: ./%s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-x <excludeFile>]\n", lowerTheString(programName));
++ printf("This program computes the taxonomic instability index.\n\nSYNTAX: %s -i <bootTrees> -n <runId> [-w <workingDir>] [-h] [-x <excludeFile>]\n", lowerTheString(programName));
+ printf("\nOBLIGATORY:\n");
+ printf("-i <bootTrees>\n\tA collection of bootstrap trees.\n");
+ printf("-n <runId>\n\tAn identifier for this run.\n");
+@@ -293,7 +293,7 @@
+ default:
+ {
+ printHelpFile();
+- abort ();
++ exit(0);
+ }
+ }
+ }
=====================================
debian/patches/hardening.patch
=====================================
@@ -7,7 +7,15 @@ Last-Update: 2017-05-01
--- a/Makefile
+++ b/Makefile
-@@ -12,12 +12,12 @@ ifeq ($(mode), profile)
+@@ -1,6 +1,6 @@
+ CC = gcc
+
+-CFLAGS = -Wall -D_GNU_SOURCE
++CFLAGS += -Wall -D_GNU_SOURCE
+ LFLAGS = -lm
+
+ ifeq ($(mode), debug)
+@@ -12,12 +12,12 @@
endif
endif
ifeq ($(mode), parallel)
@@ -23,7 +31,7 @@ Last-Update: 2017-05-01
endif
RM = rm -fr
-@@ -33,24 +33,24 @@ mast-objs = rnr-mast.o common.o List.o T
+@@ -33,24 +33,24 @@
prune-objs = rnr-prune.o common.o Tree.o BitVector.o HashTable.o legacy.o newFunctions.o List.o
rnr-lsi: $(lsi-objs)
@@ -51,7 +59,7 @@ Last-Update: 2017-05-01
%.o : %.c $(DEPS)
- $(CC) -c -o $@ $< $(CFLAGS)
-+ $(CC) -c -o $@ $< $(CPPFLAGS) $(CFLAGS) $(LDFLAGS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $< $(LDFLAGS)
clean :
$(RM) $(rnr-objs) $(lsi-objs) $(tii-objs) $(mast-objs) $(prune-objs) $(TARGETS) $(TESTS) $(rnr-test-objs) RogueNaRok-parallel
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
hardening.patch
fix-gcc10-build.patch
+fix-manpage-call-and-help-exit-code.patch
=====================================
debian/rules
=====================================
@@ -10,6 +10,6 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
override_dh_auto_build:
dh_auto_build
mv RogueNaRok roguenarok-single
- make clean
+ $(MAKE) clean
dh_auto_build -- mode=parallel
mv RogueNaRok-parallel roguenarok-parallel
=====================================
debian/tests/data/150.bs deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/data/150.tre deleted
=====================================
@@ -1 +0,0 @@
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View it on GitLab: https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2
--
View it on GitLab: https://salsa.debian.org/med-team/roguenarok/-/compare/91b469bdbdc6449a61d36a8e86c672a9695fcfc8...c5dba1bc005acbc819cf5bbe4a7d823ac53a2db2
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