This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository mcl.
commit ceec8a2cb47abf21b4d50f06fa9a8f211bb1531c Author: Andreas Tille <[email protected]> Date: Mon Jan 22 11:48:34 2018 +0100 Adapt patches to file removal --- debian/copyright | 2 +- debian/patches/series | 1 - debian/patches/spelling.patch | 328 ------------------------------------------ 3 files changed, 1 insertion(+), 330 deletions(-) diff --git a/debian/copyright b/debian/copyright index 48fb453..bb0a9cf 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,7 +1,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://micans.org/mcl/src/ Files-Excluded: */*.1 - */*.ps + */doc/*.ps */*.html */Makefile.in diff --git a/debian/patches/series b/debian/patches/series index 237d865..7f81a63 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -2,4 +2,3 @@ 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 index 074f3ff..498696b 100644 --- a/debian/patches/spelling.patch +++ b/debian/patches/spelling.patch @@ -13,24 +13,6 @@ Description: Fix spelling 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 @@ @@ -49,35 +31,6 @@ Description: Fix spelling 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 @@ @@ -89,17 +42,6 @@ Description: Fix spelling 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 @@ -122,17 +64,6 @@ Description: Fix spelling 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 @@ -155,39 +86,6 @@ Description: Fix spelling 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 @@ @@ -199,35 +97,6 @@ Description: Fix spelling \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 @@ -257,35 +126,6 @@ Description: Fix spelling 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 @@ -373,35 +213,6 @@ Description: Fix spelling \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 @@ -442,17 +253,6 @@ Description: Fix spelling .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 @@ -464,28 +264,6 @@ Description: Fix spelling } \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 @@ -497,28 +275,6 @@ Description: Fix spelling 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 @@ -577,46 +333,6 @@ Description: Fix spelling 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 @@ @@ -628,17 +344,6 @@ Description: Fix spelling } ---- 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\&. @@ -661,28 +366,6 @@ Description: Fix spelling 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 @@ -694,17 +377,6 @@ Description: Fix spelling 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mcl.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
