If I remove my boost/ directory, and attempt to build, for example, atomic, by going into libs/atomic/build and invoking b2, it fails due to a missing header: D:\tmp2\libs\atomic\build>b2 toolset=msvc-8.0 ...found 1 target... ...updating 1 target... msvc.write-setup-script C:\Users\PETERD~1\AppData\Local\Temp\b2_msvc_8.0_vcvarsall_x86.cmd ...updated 1 target... ...found 1 target... ...updating 1 target... msvc.write-setup-script C:\Users\PETERD~1\AppData\Local\Temp\b2_msvc_8.0_vcvarsall_x86_amd64.cmd ...updated 1 target... Performing configuration checks - symlinks supported : no - junctions supported : yes - hardlinks supported : yes ...found 208 targets... ...updating 5 targets... common.mkdir ..\..\..\bin.v2\libs\atomic\build\msvc-8.0\debug\threading-multi compile-c-c++ ..\..\..\bin.v2\libs\atomic\build\msvc-8.0\debug\threading-multi\lockpool.obj lockpool.cpp ..\..\..\boost/atomic/detail/ops_msvc_x86.hpp(20) : fatal error C1083: Cannot open include file: 'boost/type_traits/make_signed.hpp': No such file or directory [...] Same if I do b2 --with-atomic from root. However, if I go into, say, libs/smart_ptr/test and invoke b2 there, it works: D:\tmp2\libs\smart_ptr\test>b2 toolset=msvc-8.0 ...found 1 target... ...updating 1 target... msvc.write-setup-script C:\Users\PETERD~1\AppData\Local\Temp\b2_msvc_8.0_vcvarsa ll_x86.cmd ...updated 1 target... ...found 1 target... ...updating 1 target... msvc.write-setup-script C:\Users\PETERD~1\AppData\Local\Temp\b2_msvc_8.0_vcvarsa ll_x86_amd64.cmd ...updated 1 target... Performing configuration checks - symlinks supported : no - junctions supported : yes - hardlinks supported : yes ...patience... ...found 1722 targets... ...updating 1253 targets... common.mkdir ..\..\..\bin.v2\libs\smart_ptr common.mkdir ..\..\..\bin.v2\libs\smart_ptr\test common.mkdir ..\..\..\bin.v2\libs\smart_ptr\test\yield_k_test~mt.test common.mkdir ..\..\..\bin.v2\libs\smart_ptr\test\yield_k_test~mt.test\msvc-8.0 common.mkdir ..\..\..\bin.v2\libs\smart_ptr\test\yield_k_test~mt.test\msvc-8.0\debug common.mkdir ..\..\..\bin.v2\libs\smart_ptr\test\yield_k_test~mt.test\msvc-8.0\debug\threading-multi mklink-or-dir ..\..\..\boost\smart_ptr Junction created for ..\..\..\boost\smart_ptr <<===>> ..\include\boost\smart_ptr link.hardlink ..\..\..\boost\predef.h Hardlink created for ..\..\..\boost\predef.h <<===>> ..\..\predef\include\boost\predef.h [...] Why is that? My first thought was that this was due to the fact that I was missing libs/Jamfile.v2 (I do various "clean" installations as an experiment to see what's needed and what isn't), but I put it back there and it doesn't help.