In atualization for TeXstudio 2.9, in Kubuntu 14.04, the additional search paths (in Build tab of the config window) don't work.
I set the build commands from earlier versions of TeXstudio so that my auxiliary files are in the directory ~/.LaTeX.
This worked perfectly well until the TeXstudio 2.8.8, but in TeXstudio 2.9 stopped working (the internal viewer can not find the pdf file and the TeXstudio can not find the log file), which forced me to make a temporary downgrade to the 2.8.8.
Thanks.
Discussion: Version 2.9 seems to have broken external log paths?
Tim, can you take a look on win since it concerns the pdf search path ?
The bug resulted from incorrect merging of paths.
fixed: hg 4975 (90e516758e5c)
As a workaround in 2.9.0 you can specify the file to open in the viewer explicitly without path e.g. (in Options -> Build -> Meta Commands)
I seem to be having this same problem on windows. The viewer works if the file has no errors, but it can't find the log file.
My pdflatex command is: "C:/apps/MiKTeX 2.9/miktex/bin/pdflatex.exe" -aux-directory=C:\Windows\Temp -shell-escape -interaction=nonstopmode -synctex=1 %.tex
and I added C:\Windows\Temp to Options/Build/Additional Search Paths
Actually, maybe the viewing was broken as well without that workaround. On my downgrade to 2.8.8 things are working fine.
The above fix also corrects your issue. It will be included in all future releases (>2.9.0).