Fix Absolute Paths in Xcode

[azmfaridee]

While trying to solve the RF issue, I came across this one.

A lot of files in the project still have absolute paths like this: /Users/sarahwestcott/Desktop/mothur/source/commands/chimeravsearchcommand.cpp so when I tried compiling it in a number of Macs I got the following error in Xcode 7.3.1:

clang: error: no such file or directory: '/Users/sarahwestcott/Desktop/mothur/source/commands/chimeravsearchcommand.cpp'
clang: error: no input files

I replaced the <absolute> references with <group> and it solved the problems (stack overflow link for a similar issue http://stackoverflow.com/questions/11614919/file-in-the-project-not-seen-by-xcode-after-git-pull)

Please take a look and see if this branch properly compiles in your setup.

Detailed Log

CompileC /Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Intermediates/Mothur.build/Debug/Mothur.build/Objects-normal/x86_64/chimeravsearchcommand.o /Users/sarahwestcott/Desktop/mothur/source/commands/chimeravsearchcommand.cpp normal x86_64 c++ com.apple.compilers.llvm.clang.1_0.compiler
cd /Users/azmfaridee/Documents/Development/mothur
export LANG=en_US.US-ASCII
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang -x c++ -arch x86_64 -fmessage-length=0 -fdiagnostics-show-note-include-stack -fmacro-backtrace-limit=0 -Wno-trigraphs -fpascal-strings -O0 -Wno-missing-field-initializers -Wno-missing-prototypes -Wunreachable-code -Wno-non-virtual-dtor -Wno-overloaded-virtual -Wno-exit-time-destructors -Wno-missing-braces -Wparentheses -Wswitch -Wunused-function -Wno-unused-label -Wno-unused-parameter -Wunused-variable -Wunused-value -Wno-empty-body -Wno-uninitialized -Wno-unknown-pragmas -Wno-shadow -Wno-four-char-constants -Wno-conversion -Wno-constant-conversion -Wno-int-conversion -Wno-bool-conversion -Wno-enum-conversion -Wno-shorten-64-to-32 -Wnewline-eof -Wno-c++11-extensions -DVERSION=\"1.37.1\" -DRELEASE_DATE=\"04/11/2016\" -DMOTHUR_FILES=\"/Users/sarahwestcott/desktop/release\" -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -fasm-blocks -fstrict-aliasing -Wdeprecated-declarations -Winvalid-offsetof -mmacosx-version-min=10.11 -g -fvisibility=hidden -fvisibility-inlines-hidden -Wno-sign-conversion -I/Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Intermediates/Mothur.build/Debug/Mothur.build/mothur.hmap -I/usr/local/include -I/Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Products/Debug/include -I/Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Intermediates/Mothur.build/Debug/Mothur.build/DerivedSources/x86_64 -I/Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Intermediates/Mothur.build/Debug/Mothur.build/DerivedSources -F/Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Products/Debug -DBIT_VERSION -DUSE_BOOST -DUNIT_TEST -DUSE_READLINE -MMD -MT dependencies -MF /Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Intermediates/Mothur.build/Debug/Mothur.build/Objects-normal/x86_64/chimeravsearchcommand.d --serialize-diagnostics /Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Intermediates/Mothur.build/Debug/Mothur.build/Objects-normal/x86_64/chimeravsearchcommand.dia -c /Users/sarahwestcott/Desktop/mothur/source/commands/chimeravsearchcommand.cpp -o /Users/azmfaridee/Library/Developer/Xcode/DerivedData/Mothur-fsqhrsrbhxrejwclcotiyjafkkpr/Build/Intermediates/Mothur.build/Debug/Mothur.build/Objects-normal/x86_64/chimeravsearchcommand.o

clang: error: no such file or directory: '/Users/sarahwestcott/Desktop/mothur/source/commands/chimeravsearchcommand.cpp'
clang: error: no input files

[mothur-westcott]

Setting it to works for files like ... path = source/subsample.cpp; sourceTree = "group"; }; where you only have one directory layer.

For source files with multiple directory levels when I set it to relative to group, it's causing issues for you. It needs to be set to relative to project.

... path = source/commands/makecontigscommand.cpp; sourceTree = SOURCE_ROOT; };

The chimera.vsearch command was set relative to group in Xcode, but needed to be set relative to project to resolve the absolute path issue. Thanks for bringing this back up. New files default to relative to group and I missed it.

[mothur-westcott]

Branch 1.39.0 has the paths fixed.