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From: <tr...@us...> - 2003-02-11 06:53:54
|
Update of /cvsroot/basedb/basedb/plugins/src In directory sc8-pr-cvs1:/tmp/cvs-serv8894 Added Files: .cvsignore Log Message: Added missing .cvsignore entries --- NEW FILE: .cvsignore --- Makefile Makefile.in .deps |
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv29789/include/classes
Modified Files:
basecontrol.inc.php basefile.inc.php bioassayset.inc.php
ftpd.inc.php jobhandler.inc.php upload.inc.php
Log Message:
Work done on laptop in Gothenburg - no time for more detailed message
Index: basecontrol.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/basecontrol.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** basecontrol.inc.php 30 Jan 2003 16:44:38 -0000 1.8
--- basecontrol.inc.php 10 Feb 2003 08:40:42 -0000 1.9
***************
*** 85,102 ****
}
function awaitUp($secs = 3600)
{
! $secs = (int)$secs;
! while($secs >= 0)
{
- if($this->mayRun() && db_verify_connection())
- {
- $query = "SELECT 1 FROM BaseControl WHERE `shutDown` = 0";
[...89 lines suppressed...]
{
$query = "UPDATE BaseControl SET `shutDown` = 0 ".
"WHERE `shutDown` = 1";
+ if(!$ignorePending)
+ $query .= " AND `pendingTransactions` = 0";
if(!query($query) || db_affected_rows() != 1)
return false;
***************
*** 217,221 ****
if(!db_verify_connection())
return false;
! if(!$this->abortShutdown())
return false;
$query = "UPDATE BaseControl SET `startTime` = NOW()";
--- 236,240 ----
if(!db_verify_connection())
return false;
! if(!$this->abortShutdown(false))
return false;
$query = "UPDATE BaseControl SET `startTime` = NOW()";
Index: basefile.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/basefile.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** basefile.inc.php 1 Feb 2003 17:18:50 -0000 1.5
--- basefile.inc.php 10 Feb 2003 08:40:42 -0000 1.6
***************
*** 162,166 ****
// value is the empty string. If the file is not a BASEfile, the special
// string "NOBASE" is returned.
! function countSections($filename, &$sections, &$assays)
{
// Use the external program, which also tracks assays
--- 162,168 ----
// value is the empty string. If the file is not a BASEfile, the special
// string "NOBASE" is returned.
! // $extraFloats is an array which will contain the names of extra data
! // columns (of type float) for the bioassayset (as keys).
[...80 lines suppressed...]
! if($t[1] == "")
! $par = array();
else
! $par = explode("/", $t[1]);
! $assays[$t[0]] = array($par, $t[2]);
}
+ else
+ $assays[$t[0]] = array(array($t[0]), "");
}
}
! else if($mode == 2)
{
! $extraFloats = array_flip(explode("\t", $res[$i]));
! unset($extraFloats[""]);
}
}
+ if($mode != 2)
+ return "Invalid output from sectionCounter (case 2)";
return "";
}
Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassayset.inc.php,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** bioassayset.inc.php 3 Feb 2003 20:13:17 -0000 1.20
--- bioassayset.inc.php 10 Feb 2003 08:40:42 -0000 1.21
***************
*** 636,639 ****
--- 636,642 ----
{
global $config;
+
+ BioAssaySet::makeGeneSearchWhere($search);
+
$query = "INSERT ".
"INTO $config[dbDynamic]BioAssayData$this->experiment ".
Index: ftpd.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/ftpd.inc.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ftpd.inc.php 4 Feb 2003 18:29:48 -0000 1.2
--- ftpd.inc.php 10 Feb 2003 08:40:44 -0000 1.3
***************
*** 25,28 ****
--- 25,29 ----
require_once("user.inc.php");
require_once("upload.inc.php");
+ require_once("search.inc.php");
class ftpd
***************
*** 40,44 ****
var $dirType; // What sort of directory we're in - uploads, printmaps etc.
var $dirUser; // UserAccount object for owner of current dir, or NULL
[...1029 lines suppressed...]
+ }
+
+ if(!$this->mayAlterHere())
+ {
+ echo "550 Access denied\r\n";
+ $this->loadDirState($dirstate);
+ return;
+ }
+
+ $fname = explode("/", $arg);
+ $fname = $fname[count($fname) - 1];
+
+ $func = $this->dirType."DeleteFile";
+ $this->$func($fname);
+
+ $this->loadDirState($dirstate);
+ }
+
function comSYST()
Index: jobhandler.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/jobhandler.inc.php,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** jobhandler.inc.php 2 Feb 2003 15:31:51 -0000 1.8
--- jobhandler.inc.php 10 Feb 2003 08:40:45 -0000 1.9
***************
*** 277,281 ****
$sects = false;
$assays = false;
! $err = BaseFileInfo::countSections($jf->getName(), $sects, $assays);
if($err != "")
{
--- 277,283 ----
$sects = false;
$assays = false;
! $extraFloats = false;
! $err = BaseFileInfo::countSections($jf->getName(), $sects, $assays,
! $extraFloats);
if($err != "")
{
***************
*** 312,316 ****
if($assays)
{
! $err = $this->createChildSet($jf->getName(), $assays);
if($err != "")
$job->appendResultText($err);
--- 314,318 ----
if($assays)
{
! $err = $this->createChildSet($jf->getName(), $assays, $extraFloats);
if($err != "")
$job->appendResultText($err);
***************
*** 325,329 ****
// $assayids is an array from identifier to array(array(parents),name).
! function createChildSet($fname, &$assayids)
{
// These used to be function arguments
--- 327,331 ----
// $assayids is an array from identifier to array(array(parents),name).
! function createChildSet($fname, &$assayids, &$extraFloats)
{
// These used to be function arguments
Index: upload.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/upload.inc.php,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** upload.inc.php 4 Feb 2003 18:28:59 -0000 1.14
--- upload.inc.php 10 Feb 2003 08:40:46 -0000 1.15
***************
*** 37,41 ****
$this->fileSize = 0;
$this->mimeType = "";
! $this->addedDate = "" ? now() : strtodatetime($addedDate);
}
--- 37,42 ----
$this->fileSize = 0;
$this->mimeType = "";
! $this->addedDate =
! $addedDate == "" ? now() : strtodatetime($addedDate);
[...102 lines suppressed...]
+ function updateFileSize($val)
+ {
+ $this->fileSize = (int)$val;
+ return Item::updateColumn("Upload", $this->id, "fileSize",
+ $this->fileSize);
+ }
+
// Returns all users as an array of (id,name,lastChanged,cnt)
function getUserSummaryList(&$user)
{
$query = "SELECT ug.id, ug.name, ".
! "MAX(u.`addedDate`) AS `lastChanged`, COUNT(u.id) AS cnt ".
"FROM UserGroup ug LEFT JOIN Upload u ".
"ON ug.id = u.owner ".
Item::whereRemovedAnd("u", 0)." ".
"AND ".Item::whereShared("u", $user)." ".
+ "WHERE ".Item::whereRemoved("ug", 0)." ".
+ "AND ug.isAccount = 1 ".
"GROUP BY ug.name, ug.id ORDER BY ug.name";
$res = query($query);
|
|
From: <tr...@us...> - 2003-02-10 08:41:27
|
Update of /cvsroot/basedb/basedb/include/web In directory sc8-pr-cvs1:/tmp/cvs-serv29789/include/web Modified Files: experiment_common.inc.php Log Message: Work done on laptop in Gothenburg - no time for more detailed message Index: experiment_common.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/include/web/experiment_common.inc.php,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** experiment_common.inc.php 3 Feb 2003 20:13:07 -0000 1.23 --- experiment_common.inc.php 10 Feb 2003 08:40:46 -0000 1.24 *************** *** 794,798 **** } else if($restarted) ! $rest = "Attempted restart. Refresh will be needed."; else $rest = ""; --- 794,798 ---- } else if($restarted) ! $rest = "<br>\nAttempted restart. Refresh will be needed."; else $rest = ""; |
|
From: <tr...@us...> - 2003-02-10 08:41:27
|
Update of /cvsroot/basedb/basedb/src
In directory sc8-pr-cvs1:/tmp/cvs-serv29789/src
Modified Files:
baseftpd.c
Log Message:
Work done on laptop in Gothenburg - no time for more detailed message
Index: baseftpd.c
===================================================================
RCS file: /cvsroot/basedb/basedb/src/baseftpd.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** baseftpd.c 1 Feb 2003 12:52:53 -0000 1.1
--- baseftpd.c 10 Feb 2003 08:40:47 -0000 1.2
***************
*** 53,57 ****
char *dir = dirname(argv[0]);
! if(!chdir(dir))
{
perror("Unable to chdir to program directory");
--- 53,57 ----
char *dir = dirname(argv[0]);
! if(chdir(dir))
{
perror("Unable to chdir to program directory");
***************
*** 72,77 ****
strncpy(yourname, inet_ntoa(youraddr.sin_addr), 16);
execl(progname, progname, myname, yourname, NULL);
! fprintf(stderr, "Unable to run %s", progname);
! perror("");
}
--- 72,77 ----
strncpy(yourname, inet_ntoa(youraddr.sin_addr), 16);
execl(progname, progname, myname, yourname, NULL);
! fprintf(stderr, "Unable to run ");
! perror(progname);
}
|
|
From: <tr...@us...> - 2003-02-10 08:41:27
|
Update of /cvsroot/basedb/basedb/src/sectionCounter In directory sc8-pr-cvs1:/tmp/cvs-serv29789/src/sectionCounter Modified Files: sectionCounter.cc Log Message: Work done on laptop in Gothenburg - no time for more detailed message Index: sectionCounter.cc =================================================================== RCS file: /cvsroot/basedb/basedb/src/sectionCounter/sectionCounter.cc,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** sectionCounter.cc 6 Feb 2003 00:43:36 -0000 1.1 --- sectionCounter.cc 10 Feb 2003 08:40:48 -0000 1.2 *************** *** 2,6 **** // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ ! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. --- 2,6 ---- // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ ! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. *************** *** 25,28 **** --- 25,29 ---- #include <string> #include <map> + #include <set> #include "basefile.h" *************** *** 85,88 **** --- 86,90 ---- map<string,vector<string> > assayInfo; vector<string> assays; + set<string> extraFloats; if(!bfr.readSection(sect, true)) *************** *** 104,107 **** --- 106,118 ---- if(i != sect.headers.end()) registerAssays(assays, (*i).second); + map<string,int> sef; + if(sect.findFieldList("setExtraFloats", sef)) + { + for(map<string,int>::iterator i = sef.begin(); + i != sef.end(); i++) + { + extraFloats.insert((*i).first); + } + } } sect.subSections = 0; *************** *** 109,116 **** break; } // Output the sections and their counts for(map<string,int>::iterator i = sections.begin(); i != sections.end(); i++) cout << (*i).first << "\t" << (*i).second << "\n"; ! cout << endl; // Output the encountered assays, one per line, followed by parents // and optionally by name. --- 120,128 ---- break; } + cout << "sectionCount v1\n"; // Output the sections and their counts for(map<string,int>::iterator i = sections.begin(); i != sections.end(); i++) cout << (*i).first << "\t" << (*i).second << "\n"; ! cout << "\n"; // Output the encountered assays, one per line, followed by parents // and optionally by name. *************** *** 127,130 **** --- 139,155 ---- cout << (*i) << "\n"; } + } + cout << "\n"; + if(!extraFloats.empty()) + { + // Output the extra float column names, if any. + for(set<string>::iterator i = extraFloats.begin(); + i != extraFloats.end(); i++) + { + if(i != extraFloats.begin()) + cout << "\t"; + cout << (*i); + } + cout << "\n"; } |
|
From: <tr...@us...> - 2003-02-10 08:41:16
|
Update of /cvsroot/basedb/basedb/documentation/development In directory sc8-pr-cvs1:/tmp/cvs-serv29789/documentation/development Modified Files: plugins.txt Log Message: Work done on laptop in Gothenburg - no time for more detailed message Index: plugins.txt =================================================================== RCS file: /cvsroot/basedb/basedb/documentation/development/plugins.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** plugins.txt 22 Jan 2003 08:27:01 -0000 1.3 --- plugins.txt 10 Feb 2003 08:40:41 -0000 1.4 *************** *** 80,91 **** Next follows the spots section(s), in this case from a non-serial ! 'normal' BASEfile (serial files have multiple spot sections): section spots columns position reporter assayData ! assayFields ratio intensity2 position ! assays 2016 2017 2018 2019 % ! 2971 1001 0.561547 853 2971 0.909091 352 2971 1.1 320 2971 1.1 320 2971 The data in 'spots' sections is arranged in _columns_, and some of --- 80,93 ---- Next follows the spots section(s), in this case from a non-serial ! 'normal' BASEfile (serial files have multiple 'spots' sections, ! each with a single assay): section spots columns position reporter assayData ! assayFields ratio intensity2 position quality ! setExtraFloats quality ! assays 2016 2017 2018 % ! 2971 1001 0.561547 853 2971 1.2 0.909091 352 2971 0.7 1.1 320 2971 1.3 The data in 'spots' sections is arranged in _columns_, and some of *************** *** 94,100 **** for each of the assays. That is, the data in this example contains: position, molecule, ratio_of_assay_2016, intensity2_of_2016, ! position_of_2016, ratio_of_2017, intensity2_of_2017, ... ! (I included the quite redundant position field in the example by ! mistake.) The names of available columns and fields are shown on the plugin --- 96,102 ---- for each of the assays. That is, the data in this example contains: position, molecule, ratio_of_assay_2016, intensity2_of_2016, ! position_of_2016, quiality_of_2016, ratio_of_2017, intensity2_of_2017, ... ! (I included the quite redundant position field in this example by ! mistake.) The setExtraField header is used to tell BASE about The names of available columns and fields are shown on the plugin *************** *** 104,119 **** 'spots' section refer to the 'id' column in the 'assays' section. ! If you want to create a transformation plugin, have it output a ! BASEfile with 'spots' sections. If the file has an 'assays' section, ! the values in the 'assays' headers of the 'spots' section refer to that ! section (via the 'id' column), where you can specify the assay name ! (column 'name') and parents (column 'parents', multiple values ! separated by "/"). If there is no 'assays' section, the parents of new ! assays are taken to be given directly by the 'assays' in the 'spots' ! section. The names of the new sections will be inherited from their ! parents. The plugin must pass through the columns 'reporter' and 'position', and output fields 'intensity1', 'intensity2' and so on up to the number of ! channels in the experiment. To have a reporter list created by jobController.php, output a section --- 106,128 ---- 'spots' section refer to the 'id' column in the 'assays' section. ! If you want to create a transformation plugin, have it output a BASEfile ! with 'spots' sections. If the file has an 'assays' section, the values in ! the 'assays' headers of the 'spots' section refer to that section (via the ! 'id' column), where you can specify the assay name (column 'name') and ! parents (column 'parents', multiple values separated by "/"). If there is ! no 'assays' section, the parents of new assays are taken to be given ! directly by the 'assays' in the 'spots' section. The names of the new ! sections will be inherited from their parents. Each BASEfile output by a ! plugin will be used to generate a BioAssaySet, if it contains at least one ! 'spots' section. The plugin must pass through the columns 'reporter' and 'position', and output fields 'intensity1', 'intensity2' and so on up to the number of ! channels in the experiment. The setExtraFloats header is used to tell BASE ! about extra values that will be attached to every spot of the BioAssaySet. ! The setExtraFloats header is a tab-separated list of columns that are to ! be added to the BioAssayExtraFloat table. The union of all such columns in ! a file is what will be used, and these columns must exist in all 'spots' ! sections in the file. In the example above, the quality value for each ! spot will be saved in the database. To have a reporter list created by jobController.php, output a section |
|
From: <tr...@us...> - 2003-02-10 08:41:15
|
Update of /cvsroot/basedb/basedb/bin In directory sc8-pr-cvs1:/tmp/cvs-serv29789/bin Modified Files: startBase.php stopBase.php Added Files: base.server Log Message: Work done on laptop in Gothenburg - no time for more detailed message --- NEW FILE: base.server --- #! /bin/sh # ### BEGIN INIT INFO # Provides: base # Required-Start: mysql apache # Required-Stop: # Default-Start: 3 5 # Default-Stop: # Description: BASE, http://base.thep.lu.se ### END INIT INFO . /etc/rc.status . /etc/rc.config baseroot=/usr/local/base baseuser=base test -x "$baseroot/bin" || exit 0 rc_reset case "$1" in start) echo -n "Starting BASE: " su $baseuser -c "$baseroot/bin/startBase.php >/dev/null" rc_status -v ;; stop) echo -n "Shutting down BASE: " su $baseuser -c \ "$baseroot/bin/stopBase.php 'Shut down by the system' >/dev/null" rc_status -v ;; restart) ## If first returns OK call the second, if first or ## second command fails, set echo return value. $0 stop; sleep 1 && $0 start rc_status ;; *) echo "Usage: $0 {start|stop|restart}" exit 1 ;; esac rc_exit Index: startBase.php =================================================================== RCS file: /cvsroot/basedb/basedb/bin/startBase.php,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** startBase.php 3 Feb 2003 13:11:55 -0000 1.2 --- startBase.php 10 Feb 2003 08:40:40 -0000 1.3 *************** *** 56,60 **** if($BC->mayRun()) ! mydie("BASE is already running\n"); // Open database connection --- 56,65 ---- if($BC->mayRun()) ! { ! mydie("BASE is already running. If you did an unclean shutdown ". ! "of BASE\n". ! "(without using stopBase.php), you may want to run ". ! "checkDatabase.php\n"); ! } // Open database connection *************** *** 65,68 **** --- 70,82 ---- } unset($config["dbPassword"]); + + $state = $BC->getState(); + if($state && $state["pendingTransactions"]) + { + mydie("There are pending transactions according to the database.\n". + "The stopBase.php script may provide more information, or you\n". + "can just update the row in table BaseControl after verifying\n". + "that it's incorrect.\n"); + } if(!$BC->endShutdown()) Index: stopBase.php =================================================================== RCS file: /cvsroot/basedb/basedb/bin/stopBase.php,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** stopBase.php 3 Feb 2003 13:11:55 -0000 1.2 --- stopBase.php 10 Feb 2003 08:40:40 -0000 1.3 *************** *** 40,67 **** $BC = new BaseControl(); - if(!$BC->mayRun()) - mydie("BASE is already shut down\n"); ! // Open database connection ! db_connect($config["dbHost"], $config["dbUser"], $config["dbPassword"], $config["dbDatabase"]); unset($config["dbPassword"]); [...72 lines suppressed...] mydie("Unable to initiate shutdown\n"); ob_implicit_flush(1); ! $down = $BC->waitForShutdown(10); ! if(!$down) { ! fwrite(STDERR, "Waiting for locks (10 min max): "); ! // Wait for ten minutes ! for($i = 0; !$down && $i < 24; $i++) ! { ! fwrite(STDERR, "."); ! $down = $BC->waitForShutdown(25); ! } ! fwrite(STDERR, "\n"); } if(!$down) { ! mydie("Timed out after 10 minutes. ". "Manual intervention will be needed.\n"); } |
|
From: <tr...@us...> - 2003-02-10 08:40:58
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv29789/www
Modified Files:
index.phtml trans_create.phtml upload_list.phtml
Log Message:
Work done on laptop in Gothenburg - no time for more detailed message
Index: index.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/index.phtml,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** index.phtml 30 Jan 2003 18:02:44 -0000 1.25
--- index.phtml 10 Feb 2003 08:40:49 -0000 1.26
***************
*** 22,26 ****
//
require_once("getconfig.inc.php");
- require_once("getconfig.inc.php");
require_once("newinit.inc.php");
require_once("eventlog.inc.php");
--- 22,25 ----
Index: trans_create.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/trans_create.phtml,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** trans_create.phtml 3 Feb 2003 20:13:06 -0000 1.44
--- trans_create.phtml 10 Feb 2003 08:40:49 -0000 1.45
***************
*** 563,566 ****
--- 563,567 ----
// Get the gene search and copy it to this transformation
+ $oldsearch = new Search();
$gsearch = new Search();
if(!$oldsearch->readForUser($set->getOwner(), "gene") ||
Index: upload_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/upload_list.phtml,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** upload_list.phtml 22 Jan 2003 08:02:24 -0000 1.15
--- upload_list.phtml 10 Feb 2003 08:40:49 -0000 1.16
***************
*** 118,122 ****
echo "<p>\n";
! Upload::prepareSearch($search, $curUser, $others,
$curDisplay->getHitsPerPage(), showDelValue());
--- 118,122 ----
echo "<p>\n";
! Upload::prepareSearch($search, $curUser, $others ? -$userid : $userid,
$curDisplay->getHitsPerPage(), showDelValue());
|
|
From: <ku...@us...> - 2003-02-06 01:33:08
|
Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv19968
Modified Files:
configure.ac
Log Message:
Changes imposed to get backward autoconf/automake compatibility.
Index: configure.ac
===================================================================
RCS file: /cvsroot/basedb/basedb/configure.ac,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** configure.ac 6 Feb 2003 00:43:33 -0000 1.1
--- configure.ac 6 Feb 2003 01:33:05 -0000 1.2
***************
*** 29,34 ****
// - run 'autogen.sh'
! AC_INIT(BASE,1.2.0,bas...@li...)
! AC_CONFIG_SRCDIR([src/jobRunner/jobRunner.c])
AM_CONFIG_HEADER(config.h)
--- 29,37 ----
// - run 'autogen.sh'
! ## FIXME: The commented section seems to be more recent autoconf
[...66 lines suppressed...]
! # plugins/src/clustering/Makefile
! # plugins/src/mds/Makefile
! # plugins/src/merge_bioassays/Makefile
! # plugins/src/normalizers/Makefile
! # plugins/src/pca/Makefile
! # src/Makefile
! # src/assayImporter/Makefile
! # src/jobRunner/Makefile
! # src/lib/Makefile
! # src/sectionCounter/Makefile])
! #AC_OUTPUT
! AC_OUTPUT([Makefile
plugins/Makefile
plugins/src/Makefile
***************
*** 340,342 ****
src/lib/Makefile
src/sectionCounter/Makefile])
- AC_OUTPUT
--- 350,351 ----
|
|
From: <ku...@us...> - 2003-02-06 01:31:23
|
Update of /cvsroot/basedb/basedb/plugins/src/pca
In directory sc8-pr-cvs1:/tmp/cvs-serv19204
Modified Files:
Makefile.am
Added Files:
gnuplot_i.c
Log Message:
Forced to duplicate gnuplot_i.c for backward autoconf compatibility.
--- NEW FILE: gnuplot_i.c ---
/*-------------------------------------------------------------------------*/
/**
@file gnuplot_i.c
@author N. Devillard
@date Sep 1998
@version $Revision: 1.1 $
@brief C interface to gnuplot.
gnuplot is a freely available, command-driven graphical display tool for
Unix. It compiles and works quite well on a number of Unix flavours as
well as other operating systems. The following module enables sending
display requests to gnuplot through simple C calls.
*/
/*--------------------------------------------------------------------------*/
/*
[...682 lines suppressed...]
char title_str[GP_TITLE_SIZE] ;
if (title == NULL) {
strcpy(title_str, "no title") ;
} else {
strcpy(title_str, title) ;
}
if (h->nplots > 0) {
strcpy(plot_str, "replot") ;
} else {
strcpy(plot_str, "plot") ;
}
sprintf(cmd, "%s %s title \"%s\" with %s",
plot_str, equation, title_str, h->pstyle) ;
gnuplot_cmd(h, cmd) ;
h->nplots++ ;
return ;
}
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/pca/Makefile.am,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile.am 6 Feb 2003 00:43:35 -0000 1.2
--- Makefile.am 6 Feb 2003 01:31:20 -0000 1.3
***************
*** 3,7 ****
bin_PROGRAMS = pca
! pca_SOURCES = PCA_v01.c gnuplot_i-2.6/src/gnuplot_i.c
pca_LDADD = $(GSL_LIB) $(BLAS_LIB)
--- 3,7 ----
bin_PROGRAMS = pca
! pca_SOURCES = PCA_v01.c gnuplot_i.c
pca_LDADD = $(GSL_LIB) $(BLAS_LIB)
|
|
From: <ku...@us...> - 2003-02-06 01:00:07
|
Update of /cvsroot/basedb/basedb In directory sc8-pr-cvs1:/tmp/cvs-serv9939 Modified Files: autogen.sh Log Message: Index: autogen.sh =================================================================== RCS file: /cvsroot/basedb/basedb/autogen.sh,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** autogen.sh 5 Feb 2003 17:13:53 -0000 1.1 --- autogen.sh 6 Feb 2003 01:00:04 -0000 1.2 *************** *** 9,12 **** --- 9,13 ---- libtoolize --automake aclocal + autoheader automake --add-missing --gnu autoconf |
|
From: <ku...@us...> - 2003-02-06 00:43:38
|
Update of /cvsroot/basedb/basedb/src/sectionCounter In directory sc8-pr-cvs1:/tmp/cvs-serv4237/src/sectionCounter Added Files: Makefile.am sectionCounter.cc Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:36 kurri Exp $ bin_PROGRAMS = sectionCounter sectionCounter_SOURCES = sectionCounter.cc sectionCounter_LDADD = -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB) INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) --- NEW FILE: sectionCounter.cc --- // $Id: sectionCounter.cc,v 1.1 2003/02/06 00:43:36 kurri Exp $ // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. // // BASE is free software; you can redistribute it and/or // modify it under the terms of the GNU General Public License // as published by the Free Software Foundation; either version 2 // of the License, or (at your option) any later version. // // BASE is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program; if not, write to the Free Software [...103 lines suppressed...] '\t' << (*inf).second[1] << "\n"; } else { cout << (*i) << "\n"; } } if(bfr.getError()) { cerr << "sectionCount(): " << bfr.errText() << endl; return 2; } return 0; } int main() { return sectionCount(cin, cout, cerr); } |
|
From: <ku...@us...> - 2003-02-06 00:43:38
|
Update of /cvsroot/basedb/basedb/src/lib In directory sc8-pr-cvs1:/tmp/cvs-serv4237/src/lib Added Files: Makefile.am basefile.cc Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:35 kurri Exp $ noinst_LIBRARIES = libbase.a libbase_a_SOURCES = basefile.cc INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) --- NEW FILE: basefile.cc --- // $Id: basefile.cc,v 1.1 2003/02/06 00:43:35 kurri Exp $ // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. // // BASE is free software; you can redistribute it and/or // modify it under the terms of the GNU General Public License // as published by the Free Software Foundation; either version 2 // of the License, or (at your option) any later version. // // BASE is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program; if not, write to the Free Software [...206 lines suppressed...] int subSects = sect.subSections; while(subSects--) { if(!readSection(sect)) return false; if(!skipSection(sect)) return false; } return true; } bool BaseFileReader::readLines(vector<string> &vec) { dataEnd = false; // Kludge for compatibility. if(!readLine()) return false; while(!dataEnd) { vec.push_back(&buf[0]); if(!readLine()) return false; } return true; } |
|
From: <ku...@us...> - 2003-02-06 00:43:38
|
Update of /cvsroot/basedb/basedb/src/jobRunner In directory sc8-pr-cvs1:/tmp/cvs-serv4237/src/jobRunner Added Files: Makefile.am jobRunner.c Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:35 kurri Exp $ bin_PROGRAMS = jobRunner jobRunner_SOURCES = jobRunner.c AM_CFLAGS= -DBASEJOBUSER_UID=$(JOBRUNNER_UID) -DBASEUSER_UID=$(BASE_UID) --- NEW FILE: jobRunner.c --- // $Id: jobRunner.c,v 1.1 2003/02/06 00:43:35 kurri Exp $ // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ // Copyright (C) 2003 Carl Troein // // This file is part of BASE. // // BASE is free software; you can redistribute it and/or // modify it under the terms of the GNU General Public License // as published by the Free Software Foundation; either version 2 // of the License, or (at your option) any later version. // // BASE is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program; if not, write to the Free Software // Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. // // This program is to be installed as suid basejob (or whatever you // choose to call that user). It takes the first argument to be the // name of a plugin to run and subsequent arguments to be arguments // to that program, just like nice or time or whatnot. The plugin is // then run as the basejob user rather than the base user. If used // correctly, this will protect your BASE installation against broken // or malicious plugins, as well as against anyone who has managed to // gain access to the plugin definition page in BASE. #include <unistd.h> #include <stdio.h> #include <stdlib.h> #include <errno.h> #include <signal.h> #include <sys/types.h> extern int errno; #ifndef BASEUSER_UID #error BASEUSER_UID must be defined (as the UID of the BASE user) #endif #ifndef BASEJOBUSER_UID #error BASEJOBUSER_UID must be defined (as the UID of the BASE job user) #endif #define STRINGIFY(x) #x int main(int argc, char **argv) { uid_t uid, euid; if(argc < 2) { fprintf(stderr, "jobRunner: too few arguments\n"); return 125; } uid = getuid(); euid = geteuid(); if(uid != BASEUSER_UID) { fprintf(stderr, "jobRunner: may only be run by user " STRINGIFY(BASEUSER_UID) "\n"); errno = EINVAL; return 125; } if(euid != BASEJOBUSER_UID) { fprintf(stderr, "jobRunner: the effective (suid) UID must be " STRINGIFY(BASEJOBUSER_UID) "\n"); errno = EPERM; return 125; } if(setreuid(euid, (uid_t)-1)) { perror("jobRunner: Unable to setreuid()"); return 125; } signal(SIGHUP, SIG_IGN); execvp(argv[1], argv + 1); perror("jobRunner: plugin failed to execute"); return 125; } |
|
From: <ku...@us...> - 2003-02-06 00:43:38
|
Update of /cvsroot/basedb/basedb/src/assayImporter In directory sc8-pr-cvs1:/tmp/cvs-serv4237/src/assayImporter Added Files: Makefile.am assayImporter.cc Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:35 kurri Exp $ bin_PROGRAMS = assayImporter assayImporter_SOURCES = assayImporter.cc assayImporter_LDADD = -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB) INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) --- NEW FILE: assayImporter.cc --- // $Id: assayImporter.cc,v 1.1 2003/02/06 00:43:35 kurri Exp $ // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. // // BASE is free software; you can redistribute it and/or // modify it under the terms of the GNU General Public License // as published by the Free Software Foundation; either version 2 // of the License, or (at your option) any later version. // // BASE is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program; if not, write to the Free Software [...144 lines suppressed...] if(argc != 3) { cerr << "Syntax: assayImporter datafile channels " "<translationfile >tabfile\n"; return 1; } ifstream datain(argv[1]); if(!datain) { cerr << "Unable to open input file '" << argv[1] << "'\n"; return 1; } int channels = atoi(argv[2]); if(channels < 1 || channels > 100) { cerr << "Strange number of channels ("<<channels<<")\n"; return 1; } return assayImport(datain, cin, channels) ? 0 : 1; } |
|
From: <ku...@us...> - 2003-02-06 00:43:38
|
Update of /cvsroot/basedb/basedb/src In directory sc8-pr-cvs1:/tmp/cvs-serv4237/src Added Files: Makefile.am Removed Files: assayImporter.cc basefile.cc jobRunner.c sectionCounter.cc Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:35 kurri Exp $ SUBDIRS = lib assayImporter jobRunner sectionCounter bin_PROGRAMS = baseftpd ftpdspawner spotImageChopper tifftopnm baseftpd_SOURCES = baseftpd.c ftpdspawner_SOURCES = ftpdspawner.cc spotImageChopper_SOURCES = spotImageChopper.cc spotImageChopper_LDADD = $(PNM_LIB) $(JPEG_LIB) tifftopnm_SOURCES = shhopt.c tifftopnm.c tifftopnm_LDADD = $(MATH_LIB) $(PNM_LIB) $(TIFF_LIB) INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) --- assayImporter.cc DELETED --- --- basefile.cc DELETED --- --- jobRunner.c DELETED --- --- sectionCounter.cc DELETED --- |
|
From: <ku...@us...> - 2003-02-06 00:43:38
|
Update of /cvsroot/basedb/basedb/plugins/src/pca In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src/pca Modified Files: Makefile.am Removed Files: Makefile.in Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/pca/Makefile.am,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Makefile.am 1 Feb 2003 12:52:52 -0000 1.1 --- Makefile.am 6 Feb 2003 00:43:35 -0000 1.2 *************** *** 1,28 **** ! ## Process this file with automake to produce Makefile.in ! ## ! ## pca directory under exec/source of BASE distribution ! ## $Id$ ! ! AUTOMAKE_OPTIONS = foreign bin_PROGRAMS = pca - pca_SOURCES = PCA_v01.c gnuplot_i-2.6/src/gnuplot_i.c - pca_LDADD = $(PCA_LIBS) - - #jfr moved gnuplot_i in the top level of base src include directory - # also moved the gnuplot_i.c file to the pca directory - INCLUDES = -I$(includedir) -Ignuplot_i-2.6/src - - ## files with non-standard names to be included in the distro - EXTRA_DIST = \ - gnuplot_i-2.6/LICENSE gnuplot_i-2.6/README \ - gnuplot_i-2.6/html/doxygen.css gnuplot_i-2.6/html/gnuplot_i_c.html \ - gnuplot_i-2.6/html/gnuplot_i_c-source.html gnuplot_i-2.6/html/gnuplot_i_h.html \ - gnuplot_i-2.6/html/gnuplot_i_h-source.html gnuplot_i-2.6/html/index.html \ - gnuplot_i-2.6/html/struct__GNUPLOT_CTRL_.html \ - gnuplot_i-2.6/src/gnuplot_i.c gnuplot_i-2.6/src/gnuplot_i.h \ - gnuplot_i-2.6/test/anim.c gnuplot_i-2.6/test/example.c \ - gnuplot_i-2.6/test/sinepng.c \ - PCA_README TestBig.txt TestSmall.txt --- 1,8 ---- ! # $Id$ bin_PROGRAMS = pca + pca_SOURCES = PCA_v01.c gnuplot_i-2.6/src/gnuplot_i.c + pca_LDADD = $(GSL_LIB) $(BLAS_LIB) + INCLUDES = -Ignuplot_i-2.6/src --- Makefile.in DELETED --- |
|
From: <ku...@us...> - 2003-02-06 00:43:37
|
Update of /cvsroot/basedb/basedb/plugins/src/normalizers In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src/normalizers Added Files: Makefile.am Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:34 kurri Exp $ bin_PROGRAMS = lowess medianratio noinst_PROGRAMS = lowess_test lowess_SOURCES = lowess.cc lowess_renorm.cc lowess_LDADD = -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB) lowess_test_SOURCES = lowess.cc lowess_test.cc medianratio_SOURCES = medianratio.cc medianratio_LDADD = -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB) INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) |
|
From: <ku...@us...> - 2003-02-06 00:43:37
|
Update of /cvsroot/basedb/basedb/plugins/src/merge_bioassays In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src/merge_bioassays Modified Files: merge_bioassays.cc Added Files: Makefile.am Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:34 kurri Exp $ bin_PROGRAMS = merge_bioassays merge_bioassays_SOURCES = merge_bioassays.cc merge_bioassays_LDADD = -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB) INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) Index: merge_bioassays.cc =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/merge_bioassays/merge_bioassays.cc,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** merge_bioassays.cc 1 Feb 2003 12:52:52 -0000 1.1 --- merge_bioassays.cc 6 Feb 2003 00:43:34 -0000 1.2 *************** *** 1,4 **** #include <iostream> ! #include "../basefile.h" --- 1,4 ---- #include <iostream> ! #include "basefile.h" |
|
From: <ku...@us...> - 2003-02-06 00:43:37
|
Update of /cvsroot/basedb/basedb/plugins/src/mds In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src/mds Modified Files: Makefile.am Removed Files: Makefile.in Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/mds/Makefile.am,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Makefile.am 1 Feb 2003 12:52:52 -0000 1.1 --- Makefile.am 6 Feb 2003 00:43:34 -0000 1.2 *************** *** 1,16 **** ! ## Process this file with automake to produce Makefile.in ! ## ! ## mds directory under exec/source of BASE distribution ! ## $Id$ ! ! AUTOMAKE_OPTIONS = foreign bin_PROGRAMS = mds - mds_SOURCES = cc mds.cc mds_algo.cc MDSWrapper.cc fastsqrt.cc - mds_LDADD = ../../../src/basefile.o $(MDS_LIBS) - INCLUDES = -I../../../src/include - DEFS=-fno-exceptions -D_GNU_SOURCE ! ## files with non-standard names to be included in the distro ! EXTRA_DIST = fastsqrt.h mds_algo.h MDSWrapper.h --- 1,9 ---- ! # $Id$ bin_PROGRAMS = mds ! mds_SOURCES = mds.cc mds_algo.cc MDSWrapper.cc fastsqrt.cc ! mds_LDADD = -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB) \ ! $(GSL_LIB) $(BLAS_LIB) + INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) --- Makefile.in DELETED --- |
|
From: <ku...@us...> - 2003-02-06 00:43:37
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/source
In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src/clustering/Cgraph/source
Modified Files:
Makefile.am
Removed Files:
Makefile.in
Log Message:
Added autoconf/automake functionality. Supports c/c++ compilation.
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/source/Makefile.am,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile.am 1 Feb 2003 12:52:51 -0000 1.1
--- Makefile.am 6 Feb 2003 00:43:34 -0000 1.2
***************
*** 1,9 ****
! ## Process this file with automake to produce Makefile.in
! ##
! ## path from exec/source of base distribution:
! ## clustering/Cgraph/source
! ## $Id$
!
! AUTOMAKE_OPTIONS = foreign
lib_LIBRARIES = libcgraph.a
--- 1,3 ----
! # $Id$
lib_LIBRARIES = libcgraph.a
***************
*** 16,24 ****
cg_newfuncs.c
! INCLUDES = -I/usr/include/X11
!
! ## files with nonstandard names in this directory
! EXTRA_DIST = \
! cgaxes.h cgfont.h cglobals.h cgraph.h common.h PS_font_names.h version.h \
! Makefile.NeXT Makefile.postamble Makefile.unix
!
--- 10,12 ----
cg_newfuncs.c
! INCLUDES = -I/usr/include/X11 -I../include
--- Makefile.in DELETED ---
|
|
From: <ku...@us...> - 2003-02-06 00:43:37
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src/clustering/Cgraph Modified Files: Makefile.am Removed Files: Makefile.in Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/Makefile.am,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Makefile.am 1 Feb 2003 12:52:50 -0000 1.1 --- Makefile.am 6 Feb 2003 00:43:34 -0000 1.2 *************** *** 1,14 **** ! ## Process this file with automake to produce Makefile.in ! ## ! ## location: clustering/Cgraph from top src dir ! ## $Id$ - #jfr: examples directory should be added when the BASE install - # script is capable of doing installation tests - #SUBDIRS = examples source SUBDIRS = source - - ## files with nonstandard names to be included in the distro - EXTRA_DIST = Cgraph2.04.README README.patches - - --- 1,3 ---- ! # $Id$ SUBDIRS = source --- Makefile.in DELETED --- |
|
From: <ku...@us...> - 2003-02-06 00:43:37
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering
In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src/clustering
Modified Files:
Makefile.am
Removed Files:
Makefile.in
Log Message:
Added autoconf/automake functionality. Supports c/c++ compilation.
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/Makefile.am,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile.am 1 Feb 2003 12:52:50 -0000 1.1
--- Makefile.am 6 Feb 2003 00:43:34 -0000 1.2
***************
*** 1,36 ****
! ## Process this file with automake to produce Makefile.in
! ##
! ## clustering directory under exec/source of BASE distribution.
! ## $Id$
! AUTOMAKE_OPTIONS = foreign
! SUBDIRS = Cgraph
- bin_PROGRAMS = basehclust findsubtree drawmatrix drawgenetree drawassaytree
bin_SCRIPTS = clusteringscript
! basehclust_SOURCES = \
! basefile.cc main.cc \
AssayTree.cc BruteForce.cc Cluster.cc ClusterTree.cc CongaLine.cc \
Error.cc FastPair.cc GeneTree.cc MultiConga.cc Neighbors.cc \
NoClusteringCP.cc Quadtree.cc SortedArray.cc StoreMergeReporter.cc
! findsubtree_SOURCES = FindSubTree.cc ClusterTree.cc GeneTree.cc
! drawmatrix_SOURCES = DrawMatrix.cc ClusterTree.cc GeneTree.cc AssayTree.cc basefile.cc
! drawgenetree_SOURCES = DrawGeneTree.cc ClusterTree.cc GeneTree.cc basefile.cc
! drawassaytree_SOURCES = DrawAssayTree.cc ClusterTree.cc AssayTree.cc basefile.cc
! basehclust_LDADD = $(CLUSTERING_LIBS)
! findsubtree_LDADD = $(CLUSTERING_LIBS)
! drawmatrix_LDADD = $(CLUSTERING_LIBS)
! drawgenetree_LDADD = $(CLUSTERING_LIBS)
! drawassaytree_LDADD = $(CLUSTERING_LIBS)
! INCLUDES = -I../ -I$(includedir)
! DEFS= -fno-exceptions
! ## files with non-standard names to be included in the distro
! EXTRA_DIST = \
! Algorithms.h AllClosestPairs.h AssayAnnotation.h AssayTree.h \
! BaseClustering.h BruteForce.h ClusterTree.h ClosestPairs.h \
! Cluster.h clusteringscript CongaLine.h Distances.h Error.h \
! FastPair.h GeneTree.h MergeNode.h MergeReporter.h \
! MultiConga.h NoClusteringCP.h Neighbors.h PointSet.h \
! Quadtree.h SortedArray.h StoreMergeReporter.h Vector.h
--- 1,31 ----
! # $Id$
! SUBDIRS = Cgraph
! bin_PROGRAMS = basehclust drawassaytree drawgenetree drawmatrix findsubtree
bin_SCRIPTS = clusteringscript
!
! basehclust_SOURCES = \
! main.cc \
AssayTree.cc BruteForce.cc Cluster.cc ClusterTree.cc CongaLine.cc \
Error.cc FastPair.cc GeneTree.cc MultiConga.cc Neighbors.cc \
NoClusteringCP.cc Quadtree.cc SortedArray.cc StoreMergeReporter.cc
! basehclust_LDADD = -LCgraph/source -lcgraph \
! -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB)
! drawassaytree_SOURCES = AssayTree.cc ClusterTree.cc DrawAssayTree.cc
! drawassaytree_LDADD = -LCgraph/source -lcgraph \
! -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB)
!
! drawgenetree_SOURCES = ClusterTree.cc DrawGeneTree.cc GeneTree.cc
! drawgenetree_LDADD = -LCgraph/source -lcgraph
!
! drawmatrix_SOURCES = AssayTree.cc ClusterTree.cc DrawMatrix.cc GeneTree.cc
! drawmatrix_LDADD = -LCgraph/source -lcgraph $(GD_LIB) $(PNG_LIB) \
! -L@top_srcdir@/$(BASE_LIB_LOCATION) $(BASE_LIB)
!
! findsubtree_SOURCES = ClusterTree.cc FindSubTree.cc GeneTree.cc
! findsubtree_LDADD = -LCgraph/source -lcgraph
!
! INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) -ICgraph/include
--- Makefile.in DELETED ---
|
|
From: <ku...@us...> - 2003-02-06 00:43:36
|
Update of /cvsroot/basedb/basedb/plugins/src In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins/src Added Files: Makefile.am Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:33 kurri Exp $ SUBDIRS = clustering merge_bioassays mds normalizers pca |
|
From: <ku...@us...> - 2003-02-06 00:43:36
|
Update of /cvsroot/basedb/basedb/plugins In directory sc8-pr-cvs1:/tmp/cvs-serv4237/plugins Added Files: Makefile.am Log Message: Added autoconf/automake functionality. Supports c/c++ compilation. --- NEW FILE: Makefile.am --- # $Id: Makefile.am,v 1.1 2003/02/06 00:43:33 kurri Exp $ SUBDIRS = src |
