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From: Michael P. <mic...@ho...> - 2001-01-25 16:15:56
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Hi Jason, Here is some feedback regarding pre6...it is looking really good. There = is only one problem that really should be addressed in your script: make sure = that when an executable is supplied that it REALLY is an executable file instead = of a directory. Other than that, many of the other things are fine tuning or = documentation in the INSTALL doc. Great work! I know you'll be glad when this is over. Regards, Michael Pear ----------------------------------- ****It is possible to enter a directory name as a substitute for an = executable in the section asking program names, and it is particularly = sticky once this is done. After installing dtd2html in my local = directory not in the path, I accidentally entered /var/genex/local/bin = without pointing all the way to the executable. After that, the only way = I could recover was to edit the Bio/Genex/Config.pm file directly. Even = when I ask to answer the installation questions again, it appears that = it is checking the location of the executables rather than asking, so it = keeps finding the directory. I think this is the most critical issue = left in the installation, for those of us prone to making mistakes. ***Perl modules are still one of the most difficult to get right. I = suggest you recommend XML::Parser and XML::DOM to make sure that parser = works right before other tests. The problem with the XQL tests throws a wrinkle in because those = problems are acceptable, but ones with the XML:Parser for example = aren't. Harry noted that Class::ObjectTemplate isn't brought in = automagically through dependency when installing = Class::ObjectTemplate::DB, so you need to make those separate. **Rcluster queue_master gets mentioned, but I didn't need to start it = before to get Rcluster to work..why not? ***Also, what happens on system = reboot?=20 **Installation itself completing with no errors depends on dtd2html, it = appears, so you might as well check earlier and kick things out if the = it isn't installed. **Question reusing cached values vs. setting new values is confusing. = Currently, the formatting always throws me.I never quite know until I = read the question several times what enter will do. I suggest changing = this to a yes/no question with yes as default. "Enter/No" isn't really a = common way people look at answering questions. *Looks like all doc mods are made to INSTALL..README is out of date and = probably should be removed or changed to refer installer to INSTALL = file. *-init-dump.pl assumes write permissions for the postgres user to the = install database so that init-dump.pl can be created. Perhaps should be = noted in instructions, or can init-dump.pl be created in a tmp location = and used from there? Any other things written? *Readonly and genex passwords password not masked on entry he first = time. The genex password is requested later on and it is masked and = verified. Does it need to ask twice? *Java dependency should be noted for Jpython. Jpythonc is part of = Jpython1.1. Direct installer to look for JPython1.1 rather than = jpythonc. It isn't clear what this is used for on the server, anyways. = Can it be left out? I thought this was more of a development issue for = the dendogram applet. (It will be nice to get rid of this in a future = release, python may be a great scripting language, but you have plenty = of languages to go around at the moment in GeneX!) *Xgobi directory requested.why? Xgobi/xgvis are requested later on = independent of this request. Also, it sort of throws me off in the flow = because my first instinct when it asks for xgobi again is to enter a = directory, not the executable.=20 */usr/sbin/sendmail not detected, although it is a common location often = not in non-root user's path. *Looking for xcluster in path, but executable by default from stanford = is cluster in xcluster directory. *Missed picking up existing tmp file definition in rerun of install. = Most values are picked up and presented as defaults, but tmp file = definition is not for some reason.=20 =20 |