This is long, so here's my summary:

BLODA did indeed cause the permission denied errors while running
autogen.sh.  However, broken inverse search appears unrelated.  As for
broken inverse search, all evidence points to a regression between
1.6.1 and branch.

Now for the details.  As promised, here are the answers to your questions:

> 2) Are you running more instances of the same lyx version?

Task Manager shows a single instance of lyx.exe.

> 3) Are you sure that source specials are activated?

Yes.  Otherwise, my DVI/PDF viewer would not be giving me valid line numbers.

> 4) Version 1.6.1 (where inverse DVI search works) has been compiled by
>   you or are you using a package?

Version 1.6.1 works both when I use the package, and when I compile it myself.

> 1) Are you using the lyxpipe or the lyxsocket for communicating with lyx?

Neither.  For the purposes of debugging, I don't want to worry about
interprocess communication issues.  My script simply echos %f %l,
which I enter into the command buffer:

  server-goto-file-row /tmp/lyx_tmpdir.JL4960/lyx_tmpbuf1/LaTeXConfig.tex 191
  [LyX usually jumps to the first line, unless I'm using 1.6.1]

I did verify that both lyxsocket and lyxpipe give the same result.

$ lyxclient -g /tmp/lyx_tmpdir.JL4960/lyx_tmpbuf1/LaTeXConfig.tex 191
lyxclient: Connected to /tmp/lyx_tmpdir.JL4960/lyxsocket
INFO:server-goto-file-row
/tmp/lyx_tmpdir.JL4960/lyx_tmpbuf1/LaTeXConfig.tex 191:

$ echo 
"LYXCMD:revdvi:server-goto-file-row:/tmp/lyx_tmpdir.JL4644/lyx_tmpbuf0/LaTeXConfig.tex
191" > .lyx161src/mypipe.in
$ cat .lyx161src/mypipe.out
INFO:revdvi:server-goto-file-row:

To reiterate, any of these methods work in 1.6.1, while none work in branch.

After glancing over the code, I hypothesize that the issue might
result from "RowList rowlist" having size zero for some unknown
reason.


*Permissions errors when running autogen.sh*

As far as I can tell, those errors did result from BLODA, specifically
McAfee.  When On-Access Scanner is enabled, I can sometimes reproduce
the error.  After numerous tests of repeatedly switching it off and
on, I was unable to reproduce the error with O.A.S. disabled.

Server-goto-file-row still fails with O.A.S. disabled.

-Ben

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