[GeneX-dev] Re: Error in Testing the installation

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Dear Sakuji:

I am cc'ing this message to gen...@li... since more
experts monitor that list. We will look into this problem to determine
what could be causing this problem. Seems funny that it reports an error
on the same line (72) in TestDb.pm (which is in
GeneX-Server-1.0.4/Genex/t).

Todd Peterson
NCGR

 On Fri, 12 Oct 2001, Sakuji Toyama wrote:

>   I have attempted to install the program GeneX-Server-1.0.4 in
> my local machine. Installation proceeded without any trouble. But
> the test was failed with following comments;
> 
> t/AL_Spots..........ok                                                       
> t/AM_FactorValues...ok                                                       
> t/AM_Spots..........ok                                                       
> t/AM_SuspectSpots...ok                                                       
> t/ArrayLayout.......ok                                                       
> t/ArrayMeasurement..ok                                                       
> t/BlastHits.........ok                                                       
> t/Chromosome........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Chromosome.t line 16.
> BEGIN failed--compilation aborted at t/Chromosome.t line 16.
> t/Chromosome........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-5
>         Failed 5/5 tests, 0.00% okay
> t/Citation..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Citation.t line 16.
> BEGIN failed--compilation aborted at t/Citation.t line 16.
> t/Citation..........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-5
>         Failed 5/5 tests, 0.00% okay
> t/Contact...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Contact.t line 17.
> BEGIN failed--compilation aborted at t/Contact.t line 17.
> t/Contact...........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-5
>         Failed 5/5 tests, 0.00% okay
> t/ControlledVocab...ok                                                       
> t/DBUtils...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/DBUtils.t line 28.
> BEGIN failed--compilation aborted at t/DBUtils.t line 28.
> t/DBUtils...........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-21
>         Failed 21/21 tests, 0.00% okay
> t/ExperimentFactors.ok                                                       
> t/ExperimentSet.....ok                                                       
> t/ExternalDatabase..ok                                                       
> t/Genex.............Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Genex.t line 23.
> BEGIN failed--compilation aborted at t/Genex.t line 23.
> t/Genex.............dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-14
>         Failed 14/14 tests, 0.00% okay
> t/GenexAdmin........ok                                                       
> t/GroupLink.........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/GroupLink.t line 17.
> BEGIN failed--compilation aborted at t/GroupLink.t line 17.
> t/GroupLink.........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-4
>         Failed 4/4 tests, 0.00% okay
> t/GroupSec..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/GroupSec.t line 17.
> BEGIN failed--compilation aborted at t/GroupSec.t line 17.
> t/GroupSec..........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-5
>         Failed 5/5 tests, 0.00% okay
> t/HTMLUtils.........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/HTMLUtils.t line 17.
> BEGIN failed--compilation aborted at t/HTMLUtils.t line 17.
> t/HTMLUtils.........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-4
>         Failed 4/4 tests, 0.00% okay
> t/HotSpots..........ok                                                       
> t/Protocol..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Protocol.t line 17.
> BEGIN failed--compilation aborted at t/Protocol.t line 17.
> t/Protocol..........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-2
>         Failed 2/2 tests, 0.00% okay
> t/Sample............Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Sample.t line 17.
> BEGIN failed--compilation aborted at t/Sample.t line 17.
> t/Sample............dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-5
>         Failed 5/5 tests, 0.00% okay
> t/SampleProtocols...ok                                                       
> t/Scanner...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Scanner.t line 17.
> BEGIN failed--compilation aborted at t/Scanner.t line 17.
> t/Scanner...........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-2
>         Failed 2/2 tests, 0.00% okay
> t/Software..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Software.t line 17.
> BEGIN failed--compilation aborted at t/Software.t line 17.
> t/Software..........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-5
>         Failed 5/5 tests, 0.00% okay
> t/Species...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Species.t line 19.
> BEGIN failed--compilation aborted at t/Species.t line 19.
> t/Species...........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-9
>         Failed 9/9 tests, 0.00% okay
> t/SpotLink..........ok                                                       
> t/Spotter...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/Spotter.t line 17.
> BEGIN failed--compilation aborted at t/Spotter.t line 17.
> t/Spotter...........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-2
>         Failed 2/2 tests, 0.00% okay
> t/TL_FactorValues...ok                                                       
> t/TreatmentLevel....ok                                                       
> t/Treatment_AMs.....ok                                                       
> t/USF_ExternalDBLink.ok                                                      
> t/UserSec...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/UserSec.t line 17.
> BEGIN failed--compilation aborted at t/UserSec.t line 17.
> t/UserSec...........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-5
>         Failed 5/5 tests, 0.00% okay
> t/UserSequenceFeature.ok                                                     
> t/XMLUtils..........Using /home/stoyama/GeneX-Server-1.0.4/Genex/blib
> Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72.
> BEGIN failed--compilation aborted at t/TestDB.pm line 162.
> Compilation failed in require at t/XMLUtils.t line 16.
> BEGIN failed--compilation aborted at t/XMLUtils.t line 16.
> t/XMLUtils..........dubious                                                  
>         Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 1-31
>         Failed 31/31 tests, 0.00% okay
> Failed Test    Status Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> 
> Please teach me the way to solve this problem.
> 
> 
> genex-errors.txt:
> 
> !! System Error: Illegal seek @ line: 2502  (make -s test)
> 
> 
> Option.Reminders:
> 
> Following are the Directory and URLs you set or allowed to be set:
> CGIDIR = /home/httpd/cgi-bin 
> CGITMPDIR = /tmp/genex 
> CGITMPURL = http://cosmos.toyama.dummy.ne.jp/genex/tmp 
> CGI_ROOT_URL = http://cosmos.toyama.dummy.ne.jp/cgi-bin 
> CONTACT_EMAIL = st...@ae... 
> CURA_TOOL = genex/curation-tool 
> CYBERT_DIR = genex/cybert 
> CyberT_Demo_DIR = genex/CyberT-Demo 
> DB_NAME = genex 
> DOWNLOAD_DIR = genex/download 
> DTD2HTML = /usr/local/bin/dtd2html 
> DTD_DIR = genex/DTD 
> DTD_HTML_DIR = /usr/local/bio/genex/lib/dtd/genexml-html 
> DTD_HTML_URL = http://cosmos.toyama.dummy.ne.jp/genex/DTD/genexml-html 
> ENV_HOME = /tmp/genex 
> GENEXML_DIR = /usr/local/bio/genex/lib/dtd 
> GENEXML_URL = http://cosmos.toyama.dummy.ne.jp/genex/DTD 
> GENEX_CACHE_DIR = /usr/local/bio/genex/cache 
> GENEX_CB_CACHE_DIR = /usr/local/bio/genex/cache/db2xml/cb 
> GENEX_CGIDIR = /home/httpd/cgi-bin/genex 
> GENEX_CGI_URL = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex 
> GENEX_CONNECT = $Bio::Genex::LOCAL = 1; 
> GENEX_CURATOR = st...@ae... 
> GENEX_CUR_TOOL_DIR = /home/httpd/cgi-bin/genex/curation-tool 
> GENEX_DBMS = Pg 
> GENEX_DB_USERSEC = gevAPKZ/mAr2o 
> GENEX_DIR = genex 
> GENEX_EXAMPLE_DIR = /home/httpd/cgi-bin/genex/samples 
> GENEX_EXP_CACHE_DIR = /usr/local/bio/genex/cache/db2xml/exp 
> GENEX_EXTRALIBS = use lib q[/usr/local/bio/genex/perl5];
>  
> GENEX_GRAPHICS_URL = http://cosmos.toyama.dummy.ne.jp/genex/graphics 
> GENEX_HOST = localhost 
> GENEX_HTM_URL = http://cosmos.toyama.dummy.ne.jp/genex 
> GENEX_INSTALLSITE = /usr/local/bio/genex/perl5 
> GENEX_LOCAL = 1 
> GENEX_MAN1 = /usr/local/bio/genex/man/man1 
> GENEX_MAN3 = /usr/local/bio/genex/man/man3 
> GENEX_PORT = 5432 
> GENEX_QUERY_DIR = /home/httpd/cgi-bin/genex/gxquery 
> GENEX_RO_PASSWORD =  
> GENEX_RO_USER = readonly 
> GENEX_SECRET = Fri Oct 12 10:15:40 2001 
> GENEX_SERVER_INSTALLED_BY = st...@ae... 
> GENEX_SUBMISSION_HOME = /usr/local/bio/genex/submission 
> GENEX_SU_PASSWORD = sumi786 
> GENEX_SU_USER = genex 
> GENEX_URL_CUR_TOOL = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex/curation-
> tool 
> GENEX_URL_EXAMPLE = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex/samples 
> GENEX_URL_QUERY = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex/gxquery 
> GNUCUT = /usr/bin/cut 
> GNUINSTALL = /usr/bin/install 
> GNUMKDIR = /bin/mkdir 
> GNUSORT = /bin/sort 
> GNUTAIL = /usr/bin/tail 
> GNUTAR = /bin/tar 
> GRAPHICS_DIR = genex/graphics 
> GS = /usr/bin/gs 
> GXQUERY_DIR = genex/gxquery 
> HTMLDIR = /home/httpd/htdocs 
> HTMLTMPDIR = /home/httpd/htdocs/genex/tmp 
> HTML_ROOT_URL = http://cosmos.toyama.dummy.ne.jp 
> HTTP_ERR_LOG = /var/log/httpd/logs 
> INCLUDE_DIR = genex/include 
> JAR = /usr/local/bin/jar 
> LOCAL_BIN = /usr/local/bio/genex/bin 
> LOCAL_LIB = /usr/local/bio/genex/lib 
> LOCAL_ROOT = /usr/local/bio/genex 
> LOCAL_SHARE = /usr/local/bio/genex/share 
> LOCAL_VAR = /usr/local/bio/genex/var 
> LOGIN_DIR = genex/login 
> MAX_SYSTMP_SIZE = 15 
> MAX_TMPFILE_AGE = 24 
> MERGEM_DIR = genex/mergem 
> MPAGE = /usr/bin/mpage 
> PATH = /usr/kerberos/sbin:/opt/adabas/bin:/opt/adabas/pgm:/usr/kerberos/bin:/
> bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/usr/local/lib:/u
> sr/local/include:/usr/local/share:/usr/X11R6/bin:/usr/local/genome/bin:/usr/l
> ocal/bio/bin:/usr/local/bio/blast:/usr/local/bio/fasta34:/usr/local/bio/wu-bl
> ast2:/usr/local/bio/bin/blimpse:/usr/local/bio/wise2/bin:/usr/local/bio/charm
> /net-linux/bin:/usr/local/bio/charm/net-linux/lib:/usr/local/bio/charm/net-li
> nux/include:/usr/local/bio/autodock/bin:/usr/local/bio/autodock/utils:/usr/pg
> i/linux86/bin:/opt/schily/bin:/usr/local/Corbatools/ORBacus/bin:/usr/local/bi
> o/LigBuilder/bin:/usr/local/bio/3D_Dock/progs:/usr/local/bio/3D_Dock/scripts:
> /usr/java/jdk1.3.1_01/bin:/usr/local/bio/staden/linux-bin:/usr/local/bio/mode
> ller4/bin 
> PREFIX = /usr/local/bio/genex/perl5 
> R = /usr/local/bin/R 
> RCLUSTER_PERL_LIB = /usr/local/bio/genex/perl5/RCluster 
> RCLUST_DIR = genex/rcluster 
> RCluster_Demo_DIR = genex/RCluster-Demo 
> R_VERSION = R 1.3.1 (2001-08-31). 
> SENDMAIL = /usr/sbin/sendmail 
> START_PERL = #!/usr/bin/perl 
> SYSTMP = /tmp/genex 
> TOP_LEVEL_DIR = genex/top_level 
> VERSION_STRING = $Id: install-all.pl,v 1.84.2.6 2001/06/05 00:08:36 hjm Exp $
>   
> VNCSERVER = /usr/bin/vncserver 
> WWWHOST = cosmos.toyama.dummy.ne.jp 
> XCLUSTER =  
> XCLUSTER_DIR = genex/xcluster 
> XGOBI = /usr/local/xgobi/src/xgobi 
> XGOBID = /usr/local/src/xgobi 
> XGVIS = /usr/local/xgobi/src/xgvis 
> XML_WRITER = /usr/local/bio/genex/bin/db2xml.pl 
> 
> 
> Following are the Application Paths you set or allowed to be set:
> R = /usr/local/bin/R 
> cut = /usr/bin/cut 
> dtd2html = /usr/local/bin/dtd2html 
> gs = /usr/bin/gs 
> install = /usr/bin/install 
> jar = /usr/local/bin/jar 
> mkdir = /bin/mkdir 
> mpage = /usr/bin/mpage 
> sendmail = /usr/sbin/sendmail 
> sort = /bin/sort 
> tail = /usr/bin/tail 
> tar = /bin/tar 
> vncserver = /usr/bin/vncserver 
> xcluster =  
> xgobi = /usr/local/xgobi/src/xgobi 
> xgvis = /usr/local/xgobi/src/xgvis 
> 
> 
> Following are the ENVIRONMENT VARIABLES you set or allowed to be set:
> ENV_HOME = /tmp/genex 
> PATH = /usr/kerberos/sbin:/opt/adabas/bin:/opt/adabas/pgm:/usr/kerberos/bin:/
> bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/usr/local/lib:/u
> sr/local/include:/usr/local/share:/usr/X11R6/bin:/usr/local/genome/bin:/usr/l
> ocal/bio/bin:/usr/local/bio/blast:/usr/local/bio/fasta34:/usr/local/bio/wu-bl
> ast2:/usr/local/bio/bin/blimpse:/usr/local/bio/wise2/bin:/usr/local/bio/charm
> /net-linux/bin:/usr/local/bio/charm/net-linux/lib:/usr/local/bio/charm/net-li
> nux/include:/usr/local/bio/autodock/bin:/usr/local/bio/autodock/utils:/usr/pg
> i/linux86/bin:/opt/schily/bin:/usr/local/Corbatools/ORBacus/bin:/usr/local/bi
> o/LigBuilder/bin:/usr/local/bio/3D_Dock/progs:/usr/local/bio/3D_Dock/scripts:
> /usr/java/jdk1.3.1_01/bin:/usr/local/bio/staden/linux-bin:/usr/local/bio/mode
> ller4/bin 
> XGOBID = /usr/local/src/xgobi 
> 
>                                         Sakuji Toyama M.D.
>                                         Institute for Virus Research
>                                         Kyoto University
>                                         E-Mail: st...@vi...
> 