Time [in minutes]: 4 Platform [OS, libraries, etc.]: % uname -a Darwin northstar 13.1.0 Darwin Kernel Version 13.1.0: Thu Jan 16 19:40:37 PST 2014; root:xnu-2422.90.20~2/RELEASE_X86_64 x86_64 % g++ --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn) Target: x86_64-apple-darwin13.1.0 Thread model: posix Skill level (at least the following; tell us if you have a paper-specific skill): I can build complex software like GCC and the Linux kernel. Sequence of steps to build: * Downloaded tarball from http://research.cs.wisc.edu/wham/downloadswham-v0-1-3-tar-gz/ * Typed `make` and immediately got a working binary. * Lightly edited makefile to supress warnings (replace `-Wno-write-strings` with `-w`), and replace a single tab character with a newline, which was causing Emacs to warn about a suspicious line. With these changes, make runs flawlessly % make g++ -c -O3 -w hash.cpp g++ -c -O3 -w embedhash.cpp g++ -c -O3 -w main.cpp g++ -c -O3 -w sequence.cpp g++ -c -O3 -w aligner.cpp g++ -c -O3 -w interval.cpp g++ -c -O3 -w edit_distance.cpp g++ -c -O3 -w error.cpp g++ -c -O3 -w short.cpp g++ -c -O3 -w hitset.cpp g++ -c -O3 -w perfcounters.cpp g++ -c -O3 -w model.cpp g++ -c -O3 -w writer.cpp g++ -lpthread -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o g++ -c -O3 -w builder.cpp g++ -lpthread -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o % ./wham specify the base name. See usage message by specifying -h/--help. % ./wham-build specify the length of reads using -l SHA-1 of the downloaded files, dates of download, and URLs: http://www.cs.wisc.edu/wham/wp-content/plugins/download-monitor/download.php?id=3 Accessed on March 30 2014 SHA-1 hash is as follows e1ecc46d4ab3af47518fbdee4b8efab2c7a89bb9 wham-v0.1.5.tar.gz Detailed evaluation (including comments about running it): Although the supplied makefile causes the C++ compiler to emit several warnings, the software appears to build flawlessly. It is difficult to determine what went wrong with the Colberg et al. student. They did run g++ as sudo, which is odd but should not have caused problems. They also used GCC 4.6. I do not have this version installed on my machine, but I did confirm that the software also builds with GCC 4.2 and 4.8: % make g++-4.8 -c -O3 -w hash.cpp g++-4.8 -c -O3 -w embedhash.cpp g++-4.8 -c -O3 -w main.cpp g++-4.8 -c -O3 -w sequence.cpp g++-4.8 -c -O3 -w aligner.cpp g++-4.8 -c -O3 -w interval.cpp g++-4.8 -c -O3 -w edit_distance.cpp g++-4.8 -c -O3 -w error.cpp g++-4.8 -c -O3 -w short.cpp g++-4.8 -c -O3 -w hitset.cpp g++-4.8 -c -O3 -w perfcounters.cpp g++-4.8 -c -O3 -w model.cpp g++-4.8 -c -O3 -w writer.cpp g++-4.8 -lpthread -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o g++-4.8 -c -O3 -w builder.cpp g++-4.8 -lpthread -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o % make make g++-4.2 -c -O3 -w hash.cpp g++-4.2 -c -O3 -w embedhash.cpp g++-4.2 -c -O3 -w main.cpp g++-4.2 -c -O3 -w sequence.cpp g++-4.2 -c -O3 -w aligner.cpp g++-4.2 -c -O3 -w interval.cpp g++-4.2 -c -O3 -w edit_distance.cpp g++-4.2 -c -O3 -w error.cpp g++-4.2 -c -O3 -w short.cpp g++-4.2 -c -O3 -w hitset.cpp g++-4.2 -c -O3 -w perfcounters.cpp g++-4.2 -c -O3 -w model.cpp g++-4.2 -c -O3 -w writer.cpp g++-4.2 -lpthread -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o g++-4.2 -c -O3 -w builder.cpp g++-4.2 -lpthread -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o