[med-svn] [mcl] 04/05: Fix whatis entry in manpages
Andreas Tille
tille at debian.org
Tue Nov 28 10:12:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
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commit ef15064cafd2c2400f876bc941ee2ba0db8e2ff8
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 28 11:08:09 2017 +0100
Fix whatis entry in manpages
---
debian/changelog | 1 +
debian/patches/fix_whatis_entry.patch | 59 +++
debian/patches/series | 1 +
debian/patches/spelling.patch | 740 ++++++++++++++++++++++++++++++++++
4 files changed, 801 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index f0a35dd..cdc096c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,7 @@ mcl (1:14-137-2) UNRELEASED; urgency=medium
* DEP3
* hardening=+all
* Fix spelling
+ * Fix whatis entry in manpages
-- Andreas Tille <tille at debian.org> Tue, 20 May 2014 17:20:10 +0200
diff --git a/debian/patches/fix_whatis_entry.patch b/debian/patches/fix_whatis_entry.patch
new file mode 100644
index 0000000..47a376c
--- /dev/null
+++ b/debian/patches/fix_whatis_entry.patch
@@ -0,0 +1,59 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 20 May 2014 17:20:10 +0200
+Description: Fix whatis entry in manpages
+
+--- a/doc/clmformat.1
++++ b/doc/clmformat.1
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm format \- display cluster results in readable form
++clmformat \- display cluster results in readable form
+
+ (optionally with labels and/or cohesion and stickiness measures
+ attached)\&.
+--- a/doc/clminfo.1
++++ b/doc/clminfo.1
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm info \- compute performance measures for graphs and clusterings\&.
++clminfo \- compute performance measures for graphs and clusterings\&.
+
+ clminfo is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+--- a/doc/clmmate.1
++++ b/doc/clmmate.1
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm mate \- compute best matches between two clusterings
++clmmate \- compute best matches between two clusterings
+
+ clmmate is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+--- a/doc/clmoptics.1
++++ b/doc/clmoptics.1
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm optics \- implementation of the OPTICS reachability ordering
++clmoptics \- implementation of the OPTICS reachability ordering
+
+ clmoptics is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+--- a/doc/mcxctty.1
++++ b/doc/mcxctty.1
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-mcx ctty \- compute betweenness centrality for network nodes or network edges
++mcxctty \- compute betweenness centrality for network nodes or network edges
+ .SH SYNOPSIS
+
+ \fBmcx\ \&ctty\fP [options] [matrix-file]
diff --git a/debian/patches/series b/debian/patches/series
index 7f81a63..237d865 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@
02-wrong-interpreter-path.patch
05-manual-what-is.patch
spelling.patch
+fix_whatis_entry.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..074f3ff
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,740 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 20 May 2014 17:20:10 +0200
+Description: Fix spelling
+
+--- a/ChangeLog
++++ b/ChangeLog
+@@ -1531,7 +1531,7 @@ Tue, 03 Jun 2003
+
+ Nodes can be relabeled by specifying a map file. This makes it
+ easy and fast e.g. to do a one-pass Blast file parse, write the
+- cooccurrence data and a prefered node labeling, and then construct
++ cooccurrence data and a preferred node labeling, and then construct
+ the final matrix. The setup for transforming application-specific
+ data into raw data is this:
+
+--- a/doc/clmformat.1
++++ b/doc/clmformat.1
+@@ -381,13 +381,13 @@ This is simply the total amount of edge
+ in that cluster (corresponding to neighbours of the node in the
+ cluster) relative to the overall amount of edge weights for that node
+ (corresponding to all its neighbours)\&.
+-The coverage measure (refered to as \fBcov\fP)
++The coverage measure (referred to as \fBcov\fP)
+ is also used\&. This is similar to the projection
+ value, except that a) the coverage measure rewards the inclusion
+ of large edge weights (and penalizes the inclusion of insignificant
+ edge weights) and b) rewards node/cluster pairs for which the neighbour set
+ of the node is very similar to the cluster\&.
+-The maximum coverage measure (refered to as \fBmaxcov\fP) is similar
++The maximum coverage measure (referred to as \fBmaxcov\fP) is similar
+ to the normal coverage measure except that it rewards inclusion
+ of large edge weights even more\&.
+ The cov and maxcov performance measures have several nice continuity and
+--- a/doc/clmformat.azm
++++ b/doc/clmformat.azm
+@@ -393,13 +393,13 @@
+ in that cluster (corresponding to neighbours of the node in the
+ cluster) relative to the overall amount of edge weights for that node
+ (corresponding to all its neighbours).
+- The coverage measure (refered to as \bf{cov})
++ The coverage measure (referred to as \bf{cov})
+ is also used. This is similar to the projection
+ value, except that a) the coverage measure rewards the inclusion
+ of large edge weights (and penalizes the inclusion of insignificant
+ edge weights) and b) rewards node/cluster pairs for which the neighbour set
+ of the node is very similar to the cluster.
+- The maximum coverage measure (refered to as \bf{maxcov}) is similar
++ The maximum coverage measure (referred to as \bf{maxcov}) is similar
+ to the normal coverage measure except that it rewards inclusion
+ of large edge weights even more.
+ The cov and maxcov performance measures have several nice continuity and
+--- a/doc/clmformat.html
++++ b/doc/clmformat.html
+@@ -481,13 +481,13 @@ This is simply the total amount of edge
+ in that cluster (corresponding to neighbours of the node in the
+ cluster) relative to the overall amount of edge weights for that node
+ (corresponding to all its neighbours).
+-The coverage measure (refered to as <b>cov</b>)
++The coverage measure (referred to as <b>cov</b>)
+ is also used. This is similar to the projection
+ value, except that a) the coverage measure rewards the inclusion
+ of large edge weights (and penalizes the inclusion of insignificant
+ edge weights) and b) rewards node/cluster pairs for which the neighbour set
+ of the node is very similar to the cluster.
+-The maximum coverage measure (refered to as <b>maxcov</b>) is similar
++The maximum coverage measure (referred to as <b>maxcov</b>) is similar
+ to the normal coverage measure except that it rewards inclusion
+ of large edge weights even more.
+ The cov and maxcov performance measures have several nice continuity and
+--- a/doc/clmmate.1
++++ b/doc/clmmate.1
+@@ -91,7 +91,7 @@ clusterings\&. The other information is
+ the total number of nodes in clusters\ \&\fCi\fP and\ \&\fCj\fP
+ for example can be obtained as the sum of entries in row\ \&\fCi\fP
+ and column\ \&\fCj\fP respectively, and the difference counts
+-can then be obtained by substracting the intersection count\&.
++can then be obtained by subtracting the intersection count\&.
+ The contingency matrix can easily be computed using \fBmcx\fP;
+ e\&.g\&.
+
+--- a/doc/clmmate.azm
++++ b/doc/clmmate.azm
+@@ -70,7 +70,7 @@
+ the total number of nodes in clusters\~\v{i} and\~\v{j}
+ for example can be obtained as the sum of entries in row\~\v{i}
+ and column\~\v{j} respectively, and the difference counts
+- can then be obtained by substracting the intersection count.
++ can then be obtained by subtracting the intersection count.
+ The contingency matrix can easily be computed using \mcx;
+ e.g.}
+
+--- a/doc/clmmate.html
++++ b/doc/clmmate.html
+@@ -168,7 +168,7 @@ clusterings. The other information is im
+ the total number of nodes in clusters <tt>i</tt> and <tt>j</tt>
+ for example can be obtained as the sum of entries in row <tt>i</tt>
+ and column <tt>j</tt> respectively, and the difference counts
+-can then be obtained by substracting the intersection count.
++can then be obtained by subtracting the intersection count.
+ The contingency matrix can easily be computed using <b>mcx</b>;
+ e.g.</p>
+ <div class="verbatim">
+--- a/doc/clmprotocols.5
++++ b/doc/clmprotocols.5
+@@ -287,7 +287,7 @@ undirected, as recommended when using \f
+ result in a directed network as BLAST E-values generally differ between two
+ sequences\&. The default course of action for \fBmcxload(1)\fP is to use the
+ best value found between a pair of labels\&. The next option,
+-\fC--abc-neg-log10\fP tranforms the numerical values in the input (the BLAST
++\fC--abc-neg-log10\fP transforms the numerical values in the input (the BLAST
+ E-values) by taking the logarithm in base\ \&10 and subsequently negating the
+ sign\&. Finally, the transformed values are capped so that any E-value below
+ 1e-200 is set to a maximum allowed edge weight of\ \&200\&.
+--- a/doc/clmprotocols.azm
++++ b/doc/clmprotocols.azm
+@@ -237,7 +237,7 @@
+ result in a directed network as BLAST E-values generally differ between two
+ sequences. The default course of action for \mysib{mcxload} is to use the
+ best value found between a pair of labels. The next option,
+- \v{--abc-neg-log10} tranforms the numerical values in the input (the BLAST
++ \v{--abc-neg-log10} transforms the numerical values in the input (the BLAST
+ E-values) by taking the logarithm in base\~10 and subsequently negating the
+ sign. Finally, the transformed values are capped so that any E-value below
+ 1e-200 is set to a maximum allowed edge weight of\~200.
+--- a/doc/clmprotocols.html
++++ b/doc/clmprotocols.html
+@@ -305,7 +305,7 @@ undirected, as recommended when using <b
+ result in a directed network as BLAST E-values generally differ between two
+ sequences. The default course of action for <a class="local sibling" href="mcxload.html">mcxload</a> is to use the
+ best value found between a pair of labels. The next option,
+-<tt>--abc-neg-log10</tt> tranforms the numerical values in the input (the BLAST
++<tt>--abc-neg-log10</tt> transforms the numerical values in the input (the BLAST
+ E-values) by taking the logarithm in base 10 and subsequently negating the
+ sign. Finally, the transformed values are capped so that any E-value below
+ 1e-200 is set to a maximum allowed edge weight of 200.
+--- a/doc/clmprotocols2.5
++++ b/doc/clmprotocols2.5
+@@ -306,7 +306,7 @@ undirected, as recommended when using \f
+ result in a directed network as BLAST E-values generally differ between two
+ sequences\&. The default course of action for \fBmcxload(1)\fP is to use the
+ best value found between a pair of labels\&. The next option,
+-\fC--abc-neg-log10\fP tranforms the numerical values in the input (the BLAST
++\fC--abc-neg-log10\fP transforms the numerical values in the input (the BLAST
+ E-values) by taking the logarithm in base\ \&10 and subsequently negating the
+ sign\&. Finally, the transformed values are capped so that any E-value below
+ 1e-200 is set to a maximum allowed edge weight of\ \&200\&.
+--- a/doc/clmprotocols2.azm
++++ b/doc/clmprotocols2.azm
+@@ -222,7 +222,7 @@
+ result in a directed network as BLAST E-values generally differ between two
+ sequences. The default course of action for \mysib{mcxload} is to use the
+ best value found between a pair of labels. The next option,
+- \v{--abc-neg-log10} tranforms the numerical values in the input (the BLAST
++ \v{--abc-neg-log10} transforms the numerical values in the input (the BLAST
+ E-values) by taking the logarithm in base\~10 and subsequently negating the
+ sign. Finally, the transformed values are capped so that any E-value below
+ 1e-200 is set to a maximum allowed edge weight of\~200.
+--- a/doc/clmprotocols2.html
++++ b/doc/clmprotocols2.html
+@@ -391,7 +391,7 @@ undirected, as recommended when using <b
+ result in a directed network as BLAST E-values generally differ between two
+ sequences. The default course of action for <a class="local sibling" href="mcxload.html">mcxload</a> is to use the
+ best value found between a pair of labels. The next option,
+-<tt>--abc-neg-log10</tt> tranforms the numerical values in the input (the BLAST
++<tt>--abc-neg-log10</tt> transforms the numerical values in the input (the BLAST
+ E-values) by taking the logarithm in base 10 and subsequently negating the
+ sign. Finally, the transformed values are capped so that any E-value below
+ 1e-200 is set to a maximum allowed edge weight of 200.
+--- a/doc/distindex.html
++++ b/doc/distindex.html
+@@ -151,7 +151,7 @@
+ <td><a href="mcx.ps">ps</a></td>
+ </tr>
+ <tr>
+- <td><b>mcxsubs</b> - extract submatrices by specifiying sets of nodes and clusters</td>
++ <td><b>mcxsubs</b> - extract submatrices by specifying sets of nodes and clusters</td>
+ <td><a href="mcxsubs.html">html</a></td>
+ <td><a href="mcxsubs.ps">ps</a></td>
+ </tr>
+--- a/doc/index.html
++++ b/doc/index.html
+@@ -151,7 +151,7 @@
+ <td><a href="mcx.ps">ps</a></td>
+ </tr>
+ <tr>
+- <td><b>mcxsubs</b> - extract submatrices by specifiying sets of nodes and clusters</td>
++ <td><b>mcxsubs</b> - extract submatrices by specifying sets of nodes and clusters</td>
+ <td><a href="mcxsubs.html">html</a></td>
+ <td><a href="mcxsubs.ps">ps</a></td>
+ </tr>
+--- a/doc/index.in.azm
++++ b/doc/index.in.azm
+@@ -133,7 +133,7 @@
+ \utsection{Dealing with matrices}
+ \mkentry{mcxio}{5}{the mcl matrix format specification}
+ \mkentry{mcx}{1}{interface to basic matrix operations}
+-\mkentry{mcxsubs}{1}{extract submatrices by specifiying sets of nodes and clusters}
++\mkentry{mcxsubs}{1}{extract submatrices by specifying sets of nodes and clusters}
+ \mkentry{mcxmap}{1}{remap matrix indices / relabel graph nodes}
+ \mkentry{mcxassemble}{1}{prepare input matrix from cooccurrence scores}
+ \utend
+--- a/doc/mcl.1
++++ b/doc/mcl.1
+@@ -95,7 +95,7 @@ then it is a good idea to use native mod
+ The reason for this is that native mode is understood
+ by all programs in the mcl suite\&. It is a more stringent
+ and unambiguous format, and hence more suitable for data exchange\&.
+-The reader is refered to \fBclmprotocols(5)\fP for more information\&.
++The reader is referred to \fBclmprotocols(5)\fP for more information\&.
+ .SH SYNOPSIS
+ The example invocation below assumes matrix input, as explained above
+ and described in the \fBmcxio(5)\fP section\&. Switching to label mode requires
+@@ -540,7 +540,7 @@ file name suffix to the name of the inpu
+ 'in +2m
+ \&
+ .br
+-The first two options are somewhat outdated, in that the prefered way of
++The first two options are somewhat outdated, in that the preferred way of
+ loading networks is by using \fBmcxload(1)\fP\&. The option
+ \fB-write-expanded\fP can be useful for exploring more complicated input
+ transformations that incorporate an expansion step, but is not really
+@@ -1313,7 +1313,7 @@ will find it\&. It is less likely to wor
+ Euclidean data\&. So mcl in its canonical form is certainly not fit for
+ boundary detection or image segmentation\&. I experimented with a modified
+ mcl and boundary detection in the thesis pointed to below (see
+-\fBREFERENCES\fP)\&. This was fun and not entirely unsuccesful, but not
++\fBREFERENCES\fP)\&. This was fun and not entirely unsuccessful, but not
+ something to be pursued further\&.
+
+ \fBmcl\fP likes \fIundirected input graphs best\fP, and it really dislikes graphs
+--- a/doc/mcl.azm
++++ b/doc/mcl.azm
+@@ -91,7 +91,7 @@ by white space. The most basic example
+ The reason for this is that native mode is understood
+ by all programs in the mcl suite. It is a more stringent
+ and unambiguous format, and hence more suitable for data exchange.
+- The reader is refered to \mysib{clmprotocols} for more information.
++ The reader is referred to \mysib{clmprotocols} for more information.
+ }
+
+
+@@ -605,7 +605,7 @@ option.}
+ {\defopt{--write-limit}{write mcl process limit}}
+ }
+ \car{
+- The first two options are somewhat outdated, in that the prefered way of
++ The first two options are somewhat outdated, in that the preferred way of
+ loading networks is by using \mysib{mcxload}. The option
+ \genopt{-write-expanded} can be useful for exploring more complicated input
+ transformations that incorporate an expansion step, but is not really
+@@ -1421,7 +1421,7 @@ with value 0.8.}
+ Euclidean data. So mcl in its canonical form is certainly not fit for
+ boundary detection or image segmentation. I experimented with a modified
+ mcl and boundary detection in the thesis pointed to below (see
+- \secref{references}). This was fun and not entirely unsuccesful, but not
++ \secref{references}). This was fun and not entirely unsuccessful, but not
+ something to be pursued further.
+ }
+ \par{
+--- a/doc/mcl.html
++++ b/doc/mcl.html
+@@ -221,7 +221,7 @@ then it is a good idea to use native mod
+ The reason for this is that native mode is understood
+ by all programs in the mcl suite. It is a more stringent
+ and unambiguous format, and hence more suitable for data exchange.
+-The reader is refered to <a class="local sibling" href="clmprotocols.html">clmprotocols</a> for more information.
++The reader is referred to <a class="local sibling" href="clmprotocols.html">clmprotocols</a> for more information.
+ </p>
+
+ <a name="synopsis"></a>
+@@ -610,7 +610,7 @@ file name suffix to the name of the inpu
+ <div style="margin-top:0em"> </div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-graph"></a><b>-write-graph</b> <fname> (<i>write graph</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-graphx"></a><b>-write-graphx</b> <fname> (<i>write transformed graph</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-write-expanded"></a><b>-write-expanded</b> <fname> (<i>write expanded graph</i>)</div><d [...]
+ <div class=" item_text " style="margin-left:2em">
+ <p style="margin-top:0em; margin-bottom:0em">
+-The first two options are somewhat outdated, in that the prefered way of
++The first two options are somewhat outdated, in that the preferred way of
+ loading networks is by using <a class="local sibling" href="mcxload.html">mcxload</a>. The option
+ <b>-write-expanded</b> can be useful for exploring more complicated input
+ transformations that incorporate an expansion step, but is not really
+@@ -1234,7 +1234,7 @@ will find it. It is less likely to work
+ Euclidean data. So mcl in its canonical form is certainly not fit for
+ boundary detection or image segmentation. I experimented with a modified
+ mcl and boundary detection in the thesis pointed to below (see
+-<a class="intern" href="#references">REFERENCES</a>). This was fun and not entirely unsuccesful, but not
++<a class="intern" href="#references">REFERENCES</a>). This was fun and not entirely unsuccessful, but not
+ something to be pursued further.
+ </p>
+ <p style="margin-bottom:0" class="asd_par">
+--- a/doc/mcl.txt
++++ b/doc/mcl.txt
+@@ -59,7 +59,7 @@ mcl(1) USER COM
+ to use native mode rather than ABC mode. The reason for this is that
+ native mode is understood by all programs in the mcl suite. It is a more
+ stringent and unambiguous format, and hence more suitable for data
+- exchange. The reader is refered to clmprotocols(5) for more informa-
++ exchange. The reader is referred to clmprotocols(5) for more informa-
+ tion.
+
+ SYNOPSIS
+@@ -378,7 +378,7 @@ mcl(1) USER COM
+ -write-graphx <fname> (write transformed graph)
+ -write-expanded <fname> (write expanded graph)
+ --write-limit (write mcl process limit)
+- The first two options are somewhat outdated, in that the prefered way
++ The first two options are somewhat outdated, in that the preferred way
+ of loading networks is by using mcxload(1). The option -write-expanded
+ can be useful for exploring more complicated input transformations
+ that incorporate an expansion step, but is not really relevant for
+@@ -889,7 +889,7 @@ mcl(1) USER COM
+ from Euclidean data. So mcl in its canonical form is certainly not fit
+ for boundary detection or image segmentation. I experimented with a mod-
+ ified mcl and boundary detection in the thesis pointed to below (see
+- REFERENCES). This was fun and not entirely unsuccesful, but not some-
++ REFERENCES). This was fun and not entirely unsuccessful, but not some-
+ thing to be pursued further.
+
+ mcl likes undirected input graphs best, and it really dislikes graphs
+--- a/doc/mclfaq.7
++++ b/doc/mclfaq.7
+@@ -63,7 +63,7 @@ and mathematics behind the MCL algorithm
+ explained\&. A broad view is given in faq\ \&1\&.2,
+ and see also faq\ \&1\&.5 and section \fBREFERENCES\fP\&.
+
+-Some additional sections preceed the actual faq entries\&.
++Some additional sections precede the actual faq entries\&.
+ The TOC section contains a listing of all questions\&.
+ .SH RESOURCES
+
+@@ -532,7 +532,7 @@ Somehow, directionality thwarts the noti
+ .ZB 1m \fB3\&.11\fP
+ \s+1\fBHow do I check that my graph/matrix is symmetric/undirected?\fP\s-1
+
+-Whether your graph is created by third-party software or by custom sofware
++Whether your graph is created by third-party software or by custom software
+ written by someone you know (e\&.g\&. yourself), it is advisable to test whether
+ the software generates symmetric matrices\&. This can be done as follows
+ using the \fBmcxi utility\fP, assuming that you want to test the
+@@ -807,7 +807,7 @@ The latter two are listed when using the
+ .ZB 1m \fB6\&.2\fP
+ \s+1\fBHow do I compute the maximum amount of RAM needed by mcl?\fP\s-1
+
+-It is rougly equal to
++It is roughly equal to
+
+ .di ZV
+ .in 0
+--- a/doc/mclfaq.azm
++++ b/doc/mclfaq.azm
+@@ -36,7 +36,7 @@
+ and see also faq\~\fnum{innards} and section \secref{references}.}
+
+ \par{
+- Some additional sections preceed the actual faq entries.
++ Some additional sections precede the actual faq entries.
+ The TOC section contains a listing of all questions.
+ \${html}{
+ \bf{Clicking on the number of a question}
+@@ -374,7 +374,7 @@ dislike uni-directed graphs so much?}
+
+ \faq{checksymmetry}{How do I check that my graph/matrix is symmetric/undirected?}
+ \car{
+- Whether your graph is created by third-party software or by custom sofware
++ Whether your graph is created by third-party software or by custom software
+ written by someone you know (e.g. yourself), it is advisable to test whether
+ the software generates symmetric matrices. This can be done as follows
+ using the \sibref{mcxi}{mcxi utility}, assuming that you want to test the
+@@ -665,7 +665,7 @@ begin
+
+ \faq{}{How do I compute the maximum amount of RAM needed by mcl?}
+ \car{
+- It is rougly equal to}
++ It is roughly equal to}
+
+ \verbatim{2 * s * K * N}
+
+--- a/doc/mclfaq.html
++++ b/doc/mclfaq.html
+@@ -137,7 +137,7 @@ and mathematics behind the MCL algorithm
+ explained. A broad view is given in faq <a class="intern" href="#overview">1.2</a>,
+ and see also faq <a class="intern" href="#innards">1.5</a> and section <a class="intern" href="#references">REFERENCES</a>.</p>
+ <p style="margin-bottom:0" class="asd_par">
+-Some additional sections preceed the actual faq entries.
++Some additional sections precede the actual faq entries.
+ The TOC section contains a listing of all questions.
+ <b>Clicking on the number of a question</b>
+ (where it is answered) will take you to
+@@ -724,7 +724,7 @@ Somehow, directionality thwarts the noti
+ <div class=" item_text " style="margin-left:2em">
+ <b>How do I check that my graph/matrix is symmetric/undirected?</b>
+ <p style="margin-top:0em; margin-bottom:0em">
+-Whether your graph is created by third-party software or by custom sofware
++Whether your graph is created by third-party software or by custom software
+ written by someone you know (e.g. yourself), it is advisable to test whether
+ the software generates symmetric matrices. This can be done as follows
+ using the <a class="local sibling" href="mcxi.html">mcxi utility</a>, assuming that you want to test the
+@@ -1002,7 +1002,7 @@ The latter two are listed when using the
+ <div class=" item_text " style="margin-left:2em">
+ <b>How do I compute the maximum amount of RAM needed by mcl?</b>
+ <p style="margin-top:0em; margin-bottom:0em">
+-It is rougly equal to</p>
++It is roughly equal to</p>
+ <div class="verbatim">2 * s * K * N</div>
+ <p style="margin-top:0em; margin-bottom:0em">
+ bytes, where 2 is the number of matrices held in memory by <b>mcl</b>, s is the
+--- a/doc/mclfaq.txt
++++ b/doc/mclfaq.txt
+@@ -17,7 +17,7 @@ MCL FAQ(7) MISCELLA
+ explained. A broad view is given in faq 1.2, and see also faq 1.5
+ and section REFERENCES.
+
+- Some additional sections preceed the actual faq entries. The TOC
++ Some additional sections precede the actual faq entries. The TOC
+ section contains a listing of all questions.
+
+ RESOURCES
+@@ -366,7 +366,7 @@ MCL FAQ(7) MISCELLA
+ 3.11 How do I check that my graph/matrix is symmetric/undirected?
+
+ Whether your graph is created by third-party software or by custom
+- sofware written by someone you know (e.g. yourself), it is advisable
++ software written by someone you know (e.g. yourself), it is advisable
+ to test whether the software generates symmetric matrices. This can
+ be done as follows using the mcxi utility, assuming that you want to
+ test the matrix stored in file matrix.mci. The mcxi utility should
+@@ -600,7 +600,7 @@ MCL FAQ(7) MISCELLA
+
+ 6.2 How do I compute the maximum amount of RAM needed by mcl?
+
+- It is rougly equal to
++ It is roughly equal to
+
+ 2 * s * K * N
+
+--- a/doc/mclindex.7
++++ b/doc/mclindex.7
+@@ -143,7 +143,7 @@ interface to basic matrix operations
+ .ZI 2m "\fBmcxsubs(1)\fP"
+ \&
+ .br
+-extract submatrices by specifiying sets of nodes and clusters
++extract submatrices by specifying sets of nodes and clusters
+ .in -2m
+ .ZI 2m "\fBmcxmap(1)\fP"
+ \&
+--- a/doc/mclpipeline.1
++++ b/doc/mclpipeline.1
+@@ -516,7 +516,7 @@ relationships\&.
+ .br
+ Collect clusters in the same file until the total number
+ of nodes has exceeded \fInum\fP (in the formatted output)\&.
+-Only meaninful when \fB--fmt-fancy\fP is given\&.
++Only meaningful when \fB--fmt-fancy\fP is given\&.
+ .in -2m
+
+ .ZI 2m "\fB--fmt-tab\fP (\fIuse this tab file\fP)"
+--- a/doc/mclpipeline.azm
++++ b/doc/mclpipeline.azm
+@@ -489,7 +489,7 @@ a clustering consisting of tab-separated
+ \car{
+ Collect clusters in the same file until the total number
+ of nodes has exceeded \genarg{num} (in the formatted output).
+- Only meaninful when \genopt{--fmt-fancy} is given.
++ Only meaningful when \genopt{--fmt-fancy} is given.
+ }
+
+ \item{\defopt{--fmt-tab}{use this tab file}}
+--- a/doc/mclpipeline.html
++++ b/doc/mclpipeline.html
+@@ -574,7 +574,7 @@ relationships.
+ <p style="margin-top:0em; margin-bottom:0em">
+ Collect clusters in the same file until the total number
+ of nodes has exceeded <i>num</i> (in the formatted output).
+-Only meaninful when <b>--fmt-fancy</b> is given.
++Only meaningful when <b>--fmt-fancy</b> is given.
+ </p>
+ </div>
+ <div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--fmt-tab"></a><b>--fmt-tab</b> (<i>use this tab file</i>)</div></div>
+--- a/doc/mcxassemble.1
++++ b/doc/mcxassemble.1
+@@ -320,7 +320,7 @@ to both the column and row domains\&.
+ \fB-cmap\fP and its siblings are used to explicitly specify the
+ map file to be used, rather than combining a base name with a fixed
+ suffix\&.
+-\fB-tag\fP and its siblings work in conjuction with
++\fB-tag\fP and its siblings work in conjunction with
+ the \fB-b\fP\ \&option, and require that a tag be specified from
+ which to construct the map file (by appending it to the base name)\&.
+ .in -2m
+--- a/doc/mcxassemble.azm
++++ b/doc/mcxassemble.azm
+@@ -317,7 +317,7 @@ begin
+ \useopt{-cmap} and its siblings are used to explicitly specify the
+ map file to be used, rather than combining a base name with a fixed
+ suffix.
+- \useopt{-tag} and its siblings work in conjuction with
++ \useopt{-tag} and its siblings work in conjunction with
+ the \useopt{-b}\~option, and require that a tag be specified from
+ which to construct the map file (by appending it to the base name).
+ }
+--- a/doc/mcxassemble.html
++++ b/doc/mcxassemble.html
+@@ -380,7 +380,7 @@ to both the column and row domains.
+ <b>-cmap</b> and its siblings are used to explicitly specify the
+ map file to be used, rather than combining a base name with a fixed
+ suffix.
+-<b>-tag</b> and its siblings work in conjuction with
++<b>-tag</b> and its siblings work in conjunction with
+ the <b>-b</b> option, and require that a tag be specified from
+ which to construct the map file (by appending it to the base name).
+ </p>
+--- a/doc/mcxdeblast.html
++++ b/doc/mcxdeblast.html
+@@ -158,7 +158,7 @@ employed by <b>mclblastline</b>.</p>
+
+ <a name="stream"></a>
+ <h2>STREAM MODE</h2>
+-<p style="margin-top:0em; margin-bottom:0em">Enter stream mode by specifiying <b>--line-mode</b>=<i>abc</i>.
++<p style="margin-top:0em; margin-bottom:0em">Enter stream mode by specifying <b>--line-mode</b>=<i>abc</i>.
+ Use <b>--m9</b> if the input is in columnar output. Pipe the result
+ to a file or directly to mcl. Example invocations can be found
+ in <a class="local sibling" href="mcl.html">the mcl manual</a>.</p>
+--- a/doc/mcxio.5
++++ b/doc/mcxio.5
+@@ -34,7 +34,7 @@ mcxio \- the format specifications for i
+ The easiest format to create graphs from is a line-based format where each lines
+ represents an edge or arc\&. This format is known as the \fILarge Graph Layout\fP, as
+ \fIncol\fP format (in \fIigraph\fP), and as \fIpairwise\fP format in BioLayout\&.
+-In \fBmcl-edge\fP it is additionally refered to
++In \fBmcl-edge\fP it is additionally referred to
+ as \fIlabel\fP format or \fIabc\fP format\&.
+ In this format each line has two or three fields\&. The first two fields
+ define the source and destination node of an arc\&. Such an arc may be
+@@ -96,7 +96,7 @@ Their relative merits are described furt
+ \&
+ .br
+ This always pertains to matrices in native format concatenated in a single
+-file, refered to as a \fIcat file\fP\&. It is used for example to encode
++file, referred to as a \fIcat file\fP\&. It is used for example to encode
+ hierarchical clusterings as generated by \fBmclcm\fP\&. A cat file either
+ consists of matrices in interchange format or of matrices in binary format\&.
+ .in -2m
+@@ -160,7 +160,7 @@ utilities may be in order here\&. The pr
+ matrix functionality, the prefix \fBclm\fP is used for generic cluster
+ functionaliy\&. The \fIutility\fP \fBmcx\fP is a general purpose interpreter for
+ manipulating matrices (and grahps, sets, and clusterings)\&. The set of all
+-\fBmcl\fP siblings (cf\&. \fBmclfamily(7)\fP) is loosely refered to as the mcl
++\fBmcl\fP siblings (cf\&. \fBmclfamily(7)\fP) is loosely referred to as the mcl
+ family, which makes use of the mcl libraries (rather than the mcx
+ libraries)\&. The full truth is even more horrible, as the mcl/mcx prefix
+ conventions used in the C source code follow still other rules\&.
+--- a/doc/mcxio.azm
++++ b/doc/mcxio.azm
+@@ -28,7 +28,7 @@
+ The easiest format to create graphs from is a line-based format where each lines
+ represents an edge or arc. This format is known as the \it{Large Graph Layout}, as
+ \it{ncol} format (in \it{igraph}), and as \it{pairwise} format in BioLayout.
+- In \mcle it is additionally refered to
++ In \mcle it is additionally referred to
+ as \it{label} format or \it{abc} format.
+ In this format each line has two or three fields. The first two fields
+ define the source and destination node of an arc. Such an arc may be
+@@ -98,7 +98,7 @@
+ \item{\it{concatenated native matrix format}}
+ \car{
+ This always pertains to matrices in native format concatenated in a single
+- file, refered to as a \it{cat file}. It is used for example to encode
++ file, referred to as a \it{cat file}. It is used for example to encode
+ hierarchical clusterings as generated by \mclcm. A cat file either
+ consists of matrices in interchange format or of matrices in binary format.}
+
+@@ -164,7 +164,7 @@
+ matrix functionality, the prefix \bf{clm} is used for generic cluster
+ functionaliy. The \it{utility} \mcx is a general purpose interpreter for
+ manipulating matrices (and grahps, sets, and clusterings). The set of all
+- \mcl siblings (cf. \mysib{mclfamily}) is loosely refered to as the mcl
++ \mcl siblings (cf. \mysib{mclfamily}) is loosely referred to as the mcl
+ family, which makes use of the mcl libraries (rather than the mcx
+ libraries). The full truth is even more horrible, as the mcl/mcx prefix
+ conventions used in the C source code follow still other rules.}
+--- a/doc/mcxio.html
++++ b/doc/mcxio.html
+@@ -93,7 +93,7 @@ mcxio — the format specifications
+ The easiest format to create graphs from is a line-based format where each lines
+ represents an edge or arc. This format is known as the <i>Large Graph Layout</i>, as
+ <i>ncol</i> format (in <i>igraph</i>), and as <i>pairwise</i> format in BioLayout.
+-In <b>mcl-edge</b> it is additionally refered to
++In <b>mcl-edge</b> it is additionally referred to
+ as <i>label</i> format or <i>abc</i> format.
+ In this format each line has two or three fields. The first two fields
+ define the source and destination node of an arc. Such an arc may be
+@@ -160,7 +160,7 @@ Their relative merits are described furt
+ <div class=" item_text " style="margin-left:2em">
+ <p style="margin-top:0em; margin-bottom:0em">
+ This always pertains to matrices in native format concatenated in a single
+-file, refered to as a <i>cat file</i>. It is used for example to encode
++file, referred to as a <i>cat file</i>. It is used for example to encode
+ hierarchical clusterings as generated by <b>mclcm</b>. A cat file either
+ consists of matrices in interchange format or of matrices in binary format.</p>
+ </div>
+@@ -221,7 +221,7 @@ utilities may be in order here. The pref
+ matrix functionality, the prefix <b>clm</b> is used for generic cluster
+ functionaliy. The <i>utility</i> <b>mcx</b> is a general purpose interpreter for
+ manipulating matrices (and grahps, sets, and clusterings). The set of all
+-<b>mcl</b> siblings (cf. <a class="local sibling" href="mclfamily.html">mclfamily</a>) is loosely refered to as the mcl
++<b>mcl</b> siblings (cf. <a class="local sibling" href="mclfamily.html">mclfamily</a>) is loosely referred to as the mcl
+ family, which makes use of the mcl libraries (rather than the mcx
+ libraries). The full truth is even more horrible, as the mcl/mcx prefix
+ conventions used in the C source code follow still other rules.</p>
+--- a/doc/mcxquery.1
++++ b/doc/mcxquery.1
+@@ -293,7 +293,7 @@ and is only useful on multi-CPU machines
+ \&
+ .br
+ Output is in the form of a tab separated file\&.
+-The option \fB-icl\fP can be used in conjuction\&.
++The option \fB-icl\fP can be used in conjunction\&.
+ .in -2m
+
+ .ZI 2m "\fB-icl\fP <fname> (\fIinput clustering\fP)"
+--- a/doc/mcxquery.azm
++++ b/doc/mcxquery.azm
+@@ -279,7 +279,7 @@
+ \item{\defopt{--node-attr}{output node degree and weight attributes}}
+ \car{
+ Output is in the form of a tab separated file.
+- The option \genopt{-icl} can be used in conjuction.
++ The option \genopt{-icl} can be used in conjunction.
+ }
+
+
+--- a/doc/mcxquery.html
++++ b/doc/mcxquery.html
+@@ -350,7 +350,7 @@ and is only useful on multi-CPU machines
+ <div class=" item_text " style="margin-left:2em">
+ <p style="margin-top:0em; margin-bottom:0em">
+ Output is in the form of a tab separated file.
+-The option <b>-icl</b> can be used in conjuction.
++The option <b>-icl</b> can be used in conjunction.
+ </p>
+ </div>
+ <div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>input clustering</i>)</div></div>
+--- a/doc/tingea.log.7
++++ b/doc/tingea.log.7
+@@ -142,7 +142,7 @@ for the other units are given below\&.
+ .fi \fR
+
+ The leading tag can be used to set levels for all categories at once\&.
+-Subsequent units may then alter this intial setting\&.
++Subsequent units may then alter this initial setting\&.
+ The lead tag settings and their meaning are these:
+
+ .di ZV
+--- a/doc/tingea.log.azm
++++ b/doc/tingea.log.azm
+@@ -130,7 +130,7 @@
+
+ \car{
+ The leading tag can be used to set levels for all categories at once.
+- Subsequent units may then alter this intial setting.
++ Subsequent units may then alter this initial setting.
+ The lead tag settings and their meaning are these:}
+
+ \verbatim{\:/
+--- a/doc/tingea.log.html
++++ b/doc/tingea.log.html
+@@ -183,7 +183,7 @@ for the other units are given below.</p>
+ C SLOT3 |</div>
+ <p style="margin-top:0em; margin-bottom:0em">
+ The leading tag can be used to set levels for all categories at once.
+-Subsequent units may then alter this intial setting.
++Subsequent units may then alter this initial setting.
+ The lead tag settings and their meaning are these:</p>
+ <div class="verbatim"> 1 d1f1m1g1i1p1s1t1A1B1C1 # very yappy
+ 9 d3f4m5gxixpxsxtxAxBxCx # very terse, only d f m
+--- a/src/alien/oxygen/doc/mcxdeblast.1
++++ b/src/alien/oxygen/doc/mcxdeblast.1
+@@ -61,7 +61,7 @@ creates output files suitable for use by
+ turn create input suitable for mcl\&. This is the mode in which mcxdeblast is
+ employed by \fBmclblastline\fP\&.
+ .SH STREAM MODE
+-Enter stream mode by specifiying \fB--line-mode\fP=\fIabc\fP\&.
++Enter stream mode by specifying \fB--line-mode\fP=\fIabc\fP\&.
+ Use \fB--m9\fP if the input is in columnar output\&. Pipe the result
+ to a file or directly to mcl\&. Example invocations can be found
+ in \fBthe mcl manual\fP\&.
+--- a/src/alien/oxygen/doc/mcxdeblast.azm
++++ b/src/alien/oxygen/doc/mcxdeblast.azm
+@@ -61,7 +61,7 @@ output directly into mcl or write mcxass
+
+ \sec{stream}{STREAM MODE}
+
+-\car{Enter stream mode by specifiying \genkvp{--line-mode}{abc}.
++\car{Enter stream mode by specifying \genkvp{--line-mode}{abc}.
+ Use \genopt{--m9} if the input is in columnar output. Pipe the result
+ to a file or directly to mcl. Example invocations can be found
+ in \sibref{mcl}{the mcl manual}.}
+--- a/src/alien/oxygen/doc/mcxdeblast.html
++++ b/src/alien/oxygen/doc/mcxdeblast.html
+@@ -158,7 +158,7 @@ employed by <b>mclblastline</b>.</p>
+
+ <a name="stream"></a>
+ <h2>STREAM MODE</h2>
+-<p style="margin-top:0em; margin-bottom:0em">Enter stream mode by specifiying <b>--line-mode</b>=<i>abc</i>.
++<p style="margin-top:0em; margin-bottom:0em">Enter stream mode by specifying <b>--line-mode</b>=<i>abc</i>.
+ Use <b>--m9</b> if the input is in columnar output. Pipe the result
+ to a file or directly to mcl. Example invocations can be found
+ in <a class="local sibling" href="mcl.html">the mcl manual</a>.</p>
+--- a/src/clew/clm.c
++++ b/src/clew/clm.c
+@@ -259,7 +259,7 @@ mclx* clmMeet
+ }
+
+ if (i_clmeet != n_clmeet)
+- mcxErr(mepanic, "internal math does not substract")
++ mcxErr(mepanic, "internal math does not subtract")
+
+ ; mclxFree(&abmeet)
+ ; return clmeet
+--- a/src/impala/vector.h
++++ b/src/impala/vector.h
+@@ -546,7 +546,7 @@ mclVector* mcldMinus
+ mclVector* mcldMerge
+ ( const mclVector* lft
+ , const mclVector* rgt
+-, mclVector* dst /* values in lft prefered over rgt */
++, mclVector* dst /* values in lft preferred over rgt */
+ ) ;
+
+
+--- a/util/io.c
++++ b/util/io.c
+@@ -452,7 +452,7 @@ fprintf(stderr, "nobuffer\n")
+
+ /* fixme todo
+ *
+- * look at bc; substract it from sz (we might have read a part already).
++ * look at bc; subtract it from sz (we might have read a part already).
+ *
+ * support growing files. and look at other items in the grep source code.
+ */
--
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