Amit, I've also encountered the same issue of munging of the PATH environment variable in Windows. I haven't tracked it down yet but I suspect it has something to do with installing new versions of TPP over older versions and whether or not you delete your current TPP installation using the "add/remove programs" control panel in Windows. I've seen it also manifest itself in peculiar ways as certain TPP programs fail in unexpected places. I went so far as to put a warning message in 4.7 to at least hint at what the real problem is when this is encountered. Hopefully I will have some time to look further into what the real issue is and fix it.
As to the Linux side, the environment variable PERL_BIN is only used during the compile phase for adding the correct shell "!#" line to the perl scripts. It's suppose to be determined implicitly during the build (using "which perl") but we're finding that isn't always the case. In this particular situation buried deep in the Makefiles is an assignment that escapes PERL_BIN and used this in a string replacement on the perl scripts. I believe the problem is that PERL_BIN hasn't been set yet in the build process leaving the ESCAPED_PERL_BIN blank and resulting in the problem seen by Brian. -Joe On Wed, Mar 5, 2014 at 1:57 AM, Amit Yadav <[email protected]>wrote: > On windows 7(both 32 and 64 bit) laptop, this is a problem I have seen > many times that TPP installation overwrites the Path environment variable. > So I save the path to a file before installation, and edit it to previous > state after installing. > > I don't know if it's the same problem on Linux but can be checked by > developers. If possible, appending the TPP to path may be a better option > than overwriting it. > > -- Amit > > > On Wed, Mar 5, 2014 at 12:28 PM, Joseph Slagel < > [email protected]> wrote: > >> Brian, >> >> I was able to reproduce the problem. Its an issue how the Makefile >> deduces which perl executable you want to use. A quick fix is to just set >> PERL_BIN to be where your executable is and then rebuild TPP. Since it >> only affects perl scripts you might be able to get away with just deleting >> the .pl files from the build area and typing make again in src/. >> >> The reason we didn't catch this is our automated build is explicitly >> setting it before building. >> >> -Joe >> >> >> >> On Tue, Mar 4, 2014 at 4:55 PM, Brian Hampton <[email protected]>wrote: >> >>> Joe, >>> >>> I'm finding a number of perl files that are lacking the path to perl a >>> the top of the file. The latest one is ProphetModels.pl. >>> >>> I should recompile, but what do I change to correct this? >>> >>> Thanks in advance, >>> Brian >>> >>> >>> >>> >>> On Tue, Mar 4, 2014 at 10:49 AM, Joseph Slagel < >>> [email protected]> wrote: >>> >>>> Brian, >>>> >>>> Interesting. What's the first line in tpp_gui.pl? Does it point to a >>>> valid instance of perl on your system? Do the newlines at the end of the >>>> line look correct for Linux? And is the executable at the command line by >>>> apache (e.g. sudo -u apache /usr/local/tpp/cgi-bin/tpp_gui.pl)? >>>> >>>> -Joe >>>> >>>> >>>> >>>> On Tue, Mar 4, 2014 at 7:16 AM, Brian Hampton <[email protected]>wrote: >>>> >>>>> Hello, >>>>> >>>>> I compiled and installed TPP 4.7 as I have done for previous versions >>>>> e.g. 4.6.x on Ubuntu 12.04 but when I point my browser to cgi-bin/ >>>>> tpp_gui.pl I get an internal server error and this in the apache >>>>> error log: >>>>> >>>>> [Tue Mar 04 10:02:54 2014] [notice] Apache/2.2.22 (Ubuntu) >>>>> PHP/5.3.10-1ubuntu3.10 with Suhosin-Patch configured -- resuming normal >>>>> operations >>>>> [Tue Mar 04 10:03:12 2014] [error] [client 192.168.60.15] (2)No such >>>>> file or directory: exec of '/usr/local/tpp/cgi-bin/tpp_gui.pl' >>>>> failed, referer: http://pal.som.umaryland.edu:8080/cgi-bin/ >>>>> [Tue Mar 04 10:03:12 2014] [error] [client 192.168.60.15] Premature >>>>> end of script headers: tpp_gui.pl, referer: >>>>> http://pal.som.umaryland.edu:8080/cgi-bin/ >>>>> >>>>> >>>>> The compile from the source ended normally and without any errors. >>>>> >>>>> Brian >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To post to this group, send email to [email protected] >>>>> . >>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>> >>>> >>>> >>>> -- >>>> Joe Slagel >>>> Institute for Systems Biology >>>> [email protected] >>>> (206) 732-1362 >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> >> >> -- >> Joe Slagel >> Institute for Systems Biology >> [email protected] >> (206) 732-1362 >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
