[med-svn] [Git][med-team/raxml][master] 8 commits: d/control: declare compliance to standards version 4.7.2.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sun Mar 2 12:39:21 GMT 2025



Étienne Mollier pushed to branch master at Debian Med / raxml


Commits:
f80a307f by Étienne Mollier at 2025-03-02T12:48:13+01:00
d/control: declare compliance to standards version 4.7.2.

- - - - -
9038f996 by Étienne Mollier at 2025-03-02T13:00:39+01:00
c23.patch: new: fix build failure with gcc-15.

Closes: #1097774

- - - - -
6e0c97af by Étienne Mollier at 2025-03-02T13:04:21+01:00
d/raxmlHPC.1: fix typos caught by lintian.

- - - - -
13653688 by Étienne Mollier at 2025-03-02T13:24:47+01:00
d/raxmlHPC.1: fix groff message.

- - - - -
edd5c6a4 by Étienne Mollier at 2025-03-02T13:35:09+01:00
typos.patch: fix various typos caught by lintian.

- - - - -
f187fcc1 by Étienne Mollier at 2025-03-02T13:37:23+01:00
interpreter-path.patch: adjust perl interpreter path.

- - - - -
1163a5ed by Étienne Mollier at 2025-03-02T13:38:25+01:00
d/control: add myself to uploaders.

- - - - -
74137cb1 by Étienne Mollier at 2025-03-02T13:38:49+01:00
d/changelog: ready for upload to unstable.

- - - - -


7 changed files:

- debian/changelog
- debian/control
- + debian/patches/c23.patch
- + debian/patches/interpreter-path.patch
- debian/patches/series
- + debian/patches/typos.patch
- debian/raxmlHPC.1


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+raxml (8.2.13+dfsg-2) unstable; urgency=medium
+
+  * d/control: declare compliance to standards version 4.7.2.
+  * c23.patch: new: fix build failure with gcc-15. (Closes: #1097774)
+  * d/raxmlHPC.1: fix typos caught by lintian.
+  * d/raxmlHPC.1: fix groff message.
+  * typos.patch: fix various typos caught by lintian.
+  * interpreter-path.patch: adjust perl interpreter path.
+  * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 02 Mar 2025 13:38:42 +0100
+
 raxml (8.2.13+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -1,11 +1,12 @@
 Source: raxml
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                libsimde-dev
-Standards-Version: 4.6.2
+Standards-Version: 4.7.2.
 Vcs-Browser: https://salsa.debian.org/med-team/raxml
 Vcs-Git: https://salsa.debian.org/med-team/raxml.git
 Homepage: https://cme.h-its.org/exelixis/web/software/raxml/index.html


=====================================
debian/patches/c23.patch
=====================================
@@ -0,0 +1,22 @@
+Description: fix build failure with standard C 2023.
+ The type bool is already defined starting with standard C 2023, so it
+ is necessary to check for an old standard level before defining the
+ type.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097774
+Forwarded: https://github.com/stamatak/standard-RAxML/pull/77
+Last-Update: 2025-03-02
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- raxml.orig/rmq.h
++++ raxml/rmq.h
+@@ -10,7 +10,9 @@
+ typedef unsigned int DTidx;     // for indexing in arrays
+ typedef unsigned char DTsucc;
+ typedef unsigned short DTsucc2;
++#if !defined(__STDC_VERSION__) || __STDC_VERSION__ < 202311L
+ typedef int bool;
++#endif
+ DTidx query(DTidx, DTidx);
+ void RMQ_succinct(DT* a, DTidx n);
+ void RMQ_succinct_destroy(void);


=====================================
debian/patches/interpreter-path.patch
=====================================
@@ -0,0 +1,30 @@
+Description: Adjust Perl interpreter path.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2025-03-02
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- raxml.orig/usefulScripts/ProteinModelSelection.pl
++++ raxml/usefulScripts/ProteinModelSelection.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ 
+ #print $ARGV[0]." ".$ARGV[1]." ".$#ARGV."\n";
+ 
+--- raxml.orig/usefulScripts/applyRAxML2AllFilesInDirectory.pl
++++ raxml/usefulScripts/applyRAxML2AllFilesInDirectory.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ 
+ #print $ARGV[0]." ".$ARGV[1]." ".$#ARGV."\n";
+ 
+--- raxml.orig/usefulScripts/bsBranchLengths.pl
++++ raxml/usefulScripts/bsBranchLengths.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ 
+ print $ARGV[0]." ".$ARGV[1]." ".$ARGV[2]." ".$#ARGV."\n";
+ 


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,5 @@
 simde
 hardening
+c23.patch
+typos.patch
+interpreter-path.patch


=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,146 @@
+Description: fix typos caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/stamatak/standard-RAxML/pull/78
+Last-Update: 2025-03-02
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- raxml.orig/axml.c
++++ raxml/axml.c
+@@ -4902,7 +4902,7 @@
+   printf("                      A branch with an optimal balance does not always exist!\n");
+   printf("                      You need to specify the tree you want to root via \"-t\".\n"); 
+ 
+-  printf("              \"-f j\": generate a bunch of bootstrapped alignment files from an original alignemnt file.\n");
++  printf("              \"-f j\": generate a bunch of bootstrapped alignment files from an original alignment file.\n");
+   printf("                      You need to specify a seed with \"-b\" and the number of replicates with \"-#\" \n");   
+ 
+   printf("              \"-f J\": Compute SH-like support values on a given tree passed via \"-t\".\n"); 
+@@ -5121,7 +5121,7 @@
+   printf("             \"-I autoMRE\" for the extended majority-rule consensus tree criterion\n");
+   printf("             \"-I autoMRE_IGN\" for metrics similar to MRE, but include bipartitions under the threshold whether they are compatible\n");
+   printf("                              or not. This emulates MRE but is faster to compute.\n");
+-  printf("              You also need to pass a tree file containg several bootstrap replicates via \"-z\" \n"); 
++  printf("              You also need to pass a tree file containing several bootstrap replicates via \"-z\" \n");
+   printf("\n");
+   printf("      -j      Specifies that intermediate tree files shall be written to file during the standard ML and BS tree searches.\n");
+   printf("\n");
+@@ -5167,11 +5167,11 @@
+   printf("                                       rate categories for greater computational efficiency. Final tree might be evaluated\n");
+   printf("                                       automatically under BINGAMMA, depending on the tree search option.\n");
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+-  printf("                                       The ASC prefix willl correct the likelihood for ascertainment bias.\n");  
++  printf("                                       The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                \"-m BINGAMMA[X]\"     : GAMMA model of rate heterogeneity (alpha parameter will be estimated).\n");
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+   printf("                \"-m ASC_BINGAMMA[X]\" : GAMMA model of rate heterogeneity (alpha parameter will be estimated).\n");
+-  printf("                                       The ASC prefix willl correct the likelihood for ascertainment bias.\n");
++  printf("                                       The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+   printf("                \"-m BINGAMMAI[X]\"    : Same as BINGAMMA, but with estimate of proportion of invariable sites.\n");
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+@@ -5192,13 +5192,13 @@
+   printf("                                       rate categories for greater computational efficiency.  Final tree might be evaluated\n");
+   printf("                                       under GTRGAMMA, depending on the tree search option.\n"); 
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+-  printf("                                       The ASC prefix willl correct the likelihood for ascertainment bias.\n");  
++  printf("                                       The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                \"-m GTRGAMMA[X]\"     : GTR + Optimization of substitution rates + GAMMA model of rate \n");
+   printf("                                       heterogeneity (alpha parameter will be estimated).\n");  
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+   printf("                \"-m ASC_GTRGAMMA[X]\" : GTR + Optimization of substitution rates + GAMMA model of rate \n");
+   printf("                                       heterogeneity (alpha parameter will be estimated).\n");  
+-  printf("                                       The ASC prefix willl correct the likelihood for ascertainment bias.\n");
++  printf("                                       The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+   printf("                \"-m GTRGAMMAI[X]\"    : Same as GTRGAMMA, but with estimate of proportion of invariable sites.\n");
+   printf("                                       With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+@@ -5219,11 +5219,11 @@
+   printf("                                         rate categories for greater computational efficiency. Final tree might be evaluated\n");
+   printf("                                         automatically under MULTIGAMMA, depending on the tree search option.\n"); 
+   printf("                                         With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+-  printf("                                         The ASC prefix willl correct the likelihood for ascertainment bias.\n");  
++  printf("                                         The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                \"-m MULTIGAMMA[X]\"     : GAMMA model of rate heterogeneity (alpha parameter will be estimated).\n");
+   printf("                                         With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n"); 
+   printf("                \"-m ASC_MULTIGAMMA[X]\" : GAMMA model of rate heterogeneity (alpha parameter will be estimated).\n");
+-  printf("                                         The ASC prefix willl correct the likelihood for ascertainment bias.\n");
++  printf("                                         The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                                         With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n"); 
+   printf("                \"-m MULTIGAMMAI[X]\"    : Same as MULTIGAMMA, but with estimate of proportion of invariable sites.\n");
+   printf("                                         With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+@@ -5249,13 +5249,13 @@
+   printf("                                                    rate categories for greater computational efficiency.   Final tree might be evaluated\n");
+   printf("                                                    automatically under PROTGAMMAmatrixName[F|X], depending on the tree search option.\n");  
+   printf("                                                    With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n"); 
+-  printf("                                                    The ASC prefix willl correct the likelihood for ascertainment bias.\n");
++  printf("                                                    The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                \"-m PROTGAMMAmatrixName[F|X]\"     : specified AA matrix + Optimization of substitution rates + GAMMA model of rate \n");
+   printf("                                                    heterogeneity (alpha parameter will be estimated).\n"); 
+   printf("                                                    With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+   printf("                \"-m ASC_PROTGAMMAmatrixName[F|X]\" : specified AA matrix + Optimization of substitution rates + GAMMA model of rate \n");
+   printf("                                                    heterogeneity (alpha parameter will be estimated).\n"); 
+-  printf("                                                    The ASC prefix willl correct the likelihood for ascertainment bias.\n");
++  printf("                                                    The ASC prefix will correct the likelihood for ascertainment bias.\n");
+   printf("                                                    With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n"); 
+   printf("                \"-m PROTGAMMAImatrixName[F|X]\"    : Same as PROTGAMMAmatrixName[F|X], but with estimate of proportion of invariable sites.\n");
+   printf("                                                    With the optional \"X\" appendix you can specify a ML estimate of base frequencies.\n");  
+@@ -5416,15 +5416,15 @@
+   printf("              DEFAULT: BFGS on\n");
+   printf("\n");
+ #ifdef _NICK
+-  printf("      --asc-corr Allows to specify the type of ascertainment bias correction you wish to use. There are %d\n", NUM_ASC_CORRECTIONS);
++  printf("      --asc-corr Specify the type of ascertainment bias correction you wish to use. There are %d\n", NUM_ASC_CORRECTIONS);
+ #else
+-  printf("      --asc-corr Allows to specify the type of ascertainment bias correction you wish to use. There are %d\n", 3);
++  printf("      --asc-corr Specify the type of ascertainment bias correction you wish to use. There are %d\n", 3);
+ #endif
+   printf("                 types available:\n");
+   printf("                 --asc-corr=lewis: the standard correction by Paul Lewis\n");
+-  printf("                 --asc-corr=felsenstein: a correction introduced by Joe Felsenstein that allows to explicitely specify\n");
++  printf("                 --asc-corr=felsenstein: a correction introduced by Joe Felsenstein that allows one to explicitly specify\n");
+   printf("                                         the number of invariable sites (if known) one wants to correct for.\n");
+-  printf("                 --asc-corr=stamatakis: a correction introduced by myself that allows to explicitely specify\n");
++  printf("                 --asc-corr=stamatakis: a correction introduced by myself that allows one to explicitly specify\n");
+   printf("                                        the number of invariable sites for each character (if known) one wants to correct for.\n");
+ #ifdef _NICK
+   printf("                 --asc-corr=goldman1: 1st correction proposed by Nick Goldman\n");
+@@ -5433,7 +5433,7 @@
+   printf("                 For further details about the Goldman corrections please refer to the manual!\n");
+ #endif
+   printf("\n");
+-  printf("      --flag-check When using this option, RAxML will only check if all command line flags specifed are available and then exit\n");
++  printf("      --flag-check When using this option, RAxML will only check if all command line flags specified are available and then exit\n");
+   printf("                   with a message listing all invalid command line flags or with a message stating that all flags are valid.\n");
+   printf("\n");
+   printf("      --auto-prot=ml|bic|aic|aicc When using automatic protein model selection you can chose the criterion for selecting these models.\n");
+@@ -13931,7 +13931,7 @@
+ 	    FILE *info = myfopen(infoFileName, "ab");
+ 	    
+ 	    printBoth(info, "You are using the GTR model of AA substitution!\n");
+-	    printBoth(info, "GTR parameters for AA substiution will automatically be estimated\n");
++	    printBoth(info, "GTR parameters for AA substitution will automatically be estimated\n");
+ 	    printBoth(info, "either jointly (GTR params will be linked) or independently (when using GTR_UNLINKED) across all partitions.\n");
+ 	    printBoth(info, "WARNING: you may be over-parametrizing the model!\n\n\n");
+ 	    
+--- raxml.orig/fastSearch.c
++++ raxml/fastSearch.c
+@@ -1252,7 +1252,7 @@
+      use less then the default, e.g., -c 16 works quite well */
+ 
+   for(model = 0; model < tr->NumberOfModels; model++)
+-    printBothOpen("Partion %d number of Cats: %d\n", model, tr->partitionData[model].numberOfCategories);
++    printBothOpen("Partition %d number of Cats: %d\n", model, tr->partitionData[model].numberOfCategories);
+ 
+   /* 
+      means that we are going to do thorough insertions 
+--- raxml.orig/parsePartitions.c
++++ raxml/parsePartitions.c
+@@ -648,7 +648,7 @@
+     {
+       printf("\nError: You are not allowed to use interleaved partitions, that is, assign non-contiguous sites\n");
+       printf("to the same partition model, when pattern compression is disabled via the -H flag,\n");
+-      printf("or when pattern compression is disabled implicitely by some other option that requires it!\n\n");
++      printf("or when pattern compression is disabled implicitly by some other option that requires it!\n\n");
+       exit(-1);
+     }
+ }


=====================================
debian/raxmlHPC.1
=====================================
@@ -139,7 +139,7 @@ DEFAULT: ON
 .IP
 \fB\-f I\fR: a simple tree rooting algorithm for unrooted trees. It roots the tree by rooting it at the branch that best balances the subtree lengths (sum over branches in the subtrees) of the left and right subtree. A branch with an optimal balance does not always exist! You need to specify the tree you want to root via "\-t".
 .IP
-\fB\-f j\fR: generate a bunch of bootstrapped alignment files from an original alignemnt file. You need to specify a seed with "\-b" and the number of replicates with "\-#"
+\fB\-f j\fR: generate a bunch of bootstrapped alignment files from an original alignment file. You need to specify a seed with "\-b" and the number of replicates with "\-#"
 .IP
 \fB\-f J\fR: Compute SH\-like support values on a given tree passed via "\-t".
 .IP
@@ -228,7 +228,7 @@ changes phase
 .IP
 \fB\-I autoMRE_IGN\fR for metrics similar to MRE, but include bipartitions under the threshold whether they are compatible or not. This emulates MRE but is faster to compute.
 .IP
-You also need to pass a tree file containg several bootstrap replicates via "\-z"
+You also need to pass a tree file containing several bootstrap replicates via "\-z"
 .TP
 \fB\-j\fR
 Specifies that intermediate tree files shall be written to file during the standard ML and BS tree searches.
@@ -289,7 +289,7 @@ evolutionary rates which are categorized into numberOfCategories distinct
 rate categories for greater computational efficiency. Final tree might be evaluated
 automatically under BINGAMMA, depending on the tree search option.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 .TP
 "\-m BINGAMMA[X]"
 : GAMMA model of rate heterogeneity (alpha parameter will be estimated).
@@ -297,7 +297,7 @@ The ASC prefix willl correct the likelihood for ascertainment bias.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
 .TP
 "\-m ASC_BINGAMMA[X]" : GAMMA model of rate heterogeneity (alpha parameter will be estimated).
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
 .TP
 "\-m BINGAMMAI[X]"
@@ -330,7 +330,7 @@ evolutionary rates which are categorized into numberOfCategories distinct
 rate categories for greater computational efficiency.  Final tree might be evaluated
 under GTRGAMMA, depending on the tree search option.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 .TP
 "\-m GTRGAMMA[X]"
 : GTR + Optimization of substitution rates + GAMMA model of rate
@@ -340,7 +340,7 @@ With the optional "X" appendix you can specify a ML estimate of base frequencies
 .TP
 "\-m ASC_GTRGAMMA[X]" : GTR + Optimization of substitution rates + GAMMA model of rate
 heterogeneity (alpha parameter will be estimated).
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
 .TP
 "\-m GTRGAMMAI[X]"
@@ -373,7 +373,7 @@ evolutionary rates which are categorized into numberOfCategories distinct
 rate categories for greater computational efficiency. Final tree might be evaluated
 automatically under MULTIGAMMA, depending on the tree search option.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 .TP
 "\-m MULTIGAMMA[X]"
 : GAMMA model of rate heterogeneity (alpha parameter will be estimated).
@@ -381,7 +381,7 @@ The ASC prefix willl correct the likelihood for ascertainment bias.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
 .TP
 "\-m ASC_MULTIGAMMA[X]" : GAMMA model of rate heterogeneity (alpha parameter will be estimated).
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
 .TP
 "\-m MULTIGAMMAI[X]"
@@ -419,7 +419,7 @@ evolutionary rates which are categorized into numberOfCategories distinct
 rate categories for greater computational efficiency.   Final tree might be evaluated
 automatically under PROTGAMMAmatrixName[F|X], depending on the tree search option.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 .TP
 "\-m PROTGAMMAmatrixName[F|X]"
 : specified AA matrix + Optimization of substitution rates + GAMMA model of rate
@@ -429,7 +429,7 @@ With the optional "X" appendix you can specify a ML estimate of base frequencies
 .TP
 "\-m ASC_PROTGAMMAmatrixName[F|X]" : specified AA matrix + Optimization of substitution rates + GAMMA model of rate
 heterogeneity (alpha parameter will be estimated).
-The ASC prefix willl correct the likelihood for ascertainment bias.
+The ASC prefix will correct the likelihood for ascertainment bias.
 With the optional "X" appendix you can specify a ML estimate of base frequencies.
 .TP
 "\-m PROTGAMMAImatrixName[F|X]"
@@ -600,18 +600,18 @@ DEFAULT: Off
 .IP
 DEFAULT: BFGS on
 .HP
-\fB\-\-asc\-corr\fR Allows to specify the type of ascertainment bias correction you wish to use. There are 3
+\fB\-\-asc\-corr\fR Specify the type of ascertainment bias correction you wish to use. There are 3
 .IP
 types available:
 \fB\-\-asc\-corr\fR=\fI\,lewis\/\fR: the standard correction by Paul Lewis
-\fB\-\-asc\-corr\fR=\fI\,felsenstein\/\fR: a correction introduced by Joe Felsenstein that allows to explicitely specify
+\fB\-\-asc\-corr\fR=\fI\,felsenstein\/\fR: a correction introduced by Joe Felsenstein that allows one to explicitly specify
 .IP
 the number of invariable sites (if known) one wants to correct for.
 .TP
-\fB\-\-asc\-corr\fR=\fI\,stamatakis\/\fR: a correction introduced by myself that allows to explicitely specify
+\fB\-\-asc\-corr\fR=\fI\,stamatakis\/\fR: a correction introduced by myself that allows one to explicitly specify
 the number of invariable sites for each character (if known) one wants to correct for.
 .HP
-\fB\-\-flag\-check\fR When using this option, RAxML will only check if all command line flags specifed are available and then exit
+\fB\-\-flag\-check\fR When using this option, RAxML will only check if all command line flags specified are available and then exit
 .IP
 with a message listing all invalid command line flags or with a message stating that all flags are valid.
 .HP
@@ -678,7 +678,7 @@ This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.
 .P
 The code itself was written by Alexandros Stamatakis.
-.pp
+.PP
 With greatly appreciated code contributions by:
 .IP
 Andre Aberer      (HITS)



View it on GitLab: https://salsa.debian.org/med-team/raxml/-/compare/c5f574ac5dabffa3829cf2c9942298f81738bdde...74137cb1c767f4ee9f056f0f9d83b544f574fdba

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