<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Dear Clemens,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Thank you very much for your response.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">When I typed /usr/local/ccp4-6.1.1/lib, it looks fine.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">There are the other errors in the Section 6.6 : httpd setup.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><blockquote type="cite"><font class="Apple-style-span" color="#000000">**************************************************************</font></blockquote></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">NOTE : The http deamon is now installed and configured.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><font class="Apple-style-span" color="#000000"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">Do you want to start the httpd now ? [y]es/[n]o > y</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">Error: Apache has not been designed to serve pages while</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">running as root. There are known race conditions that</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">will allow any local user to read any file on the system.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">If you still desire to serve pages as root then</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">add -DBIG_SECURITY_HOLE to the EXTRA_CFLAGS line in your</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">src/Configuration file and rebuild the server. It is</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">strongly suggested that you instead modify the User</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">directive in your httpd.conf file to list a non-root</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">user.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><font class="Apple-style-span" color="#000000"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">ERROR : something went wrong - please see any message above</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">and also try running the httpd binary</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">/usr/local/xtal/sharp/helpers/darwin/httpd by hand.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">Maybe this binary isn't working on that particular</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">platform/operating system? See the file(s)</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">/usr/local/xtal/sharp/helpers/*/httpd.README_GPhL.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><font class="Apple-style-span" color="#000000"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><font class="Apple-style-span" color="#000000"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">NOTE : unable to start httpd on this port - try next one</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><font class="Apple-style-span" color="#000000"><br></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">Continue [y]es/[n]o/[e]xit/[s]kip ></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><blockquote type="cite"><font class="Apple-style-span" color="#000000">***************************************************************</font></blockquote></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">I am afraid I do not know how to run this by hand.</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Do I need to do something with</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">/usr/local/xtal/sharp/helpers/darwin/httpd.README_GPhL ?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Best regards,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; ">Masato</div><div><br></div><div><br></div><div><div>On 27 Mar 2009, at 08:07, Clemens Vonrhein wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Masato,<br><br>On Fri, Mar 27, 2009 at 01:10:23AM +0000, Masato Akutsu wrote:<br><blockquote type="cite">However, I got another WARNING message at the section of server setup as <br></blockquote><blockquote type="cite">below.<br></blockquote><blockquote type="cite">4. list of directories for<br></blockquote><blockquote type="cite"> LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :<br></blockquote><blockquote type="cite"> [/usr/local/ccp4-6.1.1/share/XIAROOT/xia2//binaries/mac_386:] ><br></blockquote><blockquote type="cite"> WARNING : invalid answer - try again.<br></blockquote><br>Yes, that installation part is maybe a bit picky: it basically tests<br>that each directory in that DYLD_LIBRARY_PATH variable (picked up rom<br>your environment) exists. So there are two possible explanations:<br><br> a) the directory<br> /usr/local/ccp4-6.1.1/share/XIAROOT/xia2//binaries/mac_386 doesnt<br> exist<br><br> b) it is confused by that extra ':' at the end<br><br><blockquote type="cite">I would be most grateful if anyone could give me a hint.<br></blockquote><br>Ideally, try fixing your DYLD_LIBRARY_PATH settings before running<br>'installSHARP -F'. I'm not sure where this is set (maybe in one of the<br>CCP4 setup scripts?) though.<br><br>Or when you get stuck at that point, give it a valid entry like<br><br> /usr/local/ccp4-6.1.1/share/XIAROOT/xia2/binaries/mac_386<br><br>(i.e. without the trailing ':').<br><br>Cheers<br><br>Clemens<br><br>-- <br><br>***************************************************************<br>* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com<br>*<br>* Global Phasing Ltd.<br>* Sheraton House, Castle Park <br>* Cambridge CB3 0AX, UK<br>*--------------------------------------------------------------<br>* BUSTER Development Group (<a href="http://www.globalphasing.com">http://www.globalphasing.com</a>)<br>***************************************************************<br></div></blockquote></div><br></body></html>