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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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gramtools no longer compiles on refactor_bidir_bwd #48

Closed iqbal-lab closed 7 years ago

iqbal-lab commented 7 years ago

I get this

bash-4.1$ make Scanning dependencies of target gram make[2]: Warning: File CMakeFiles/gram.dir/depend.make' has modification time 39 s in the future [ 4%] Building CXX object CMakeFiles/gram.dir/src/map.cpp.o [ 8%] Building CXX object CMakeFiles/gram.dir/src/kmers.cpp.o [ 12%] Building CXX object CMakeFiles/gram.dir/src/bidir_search_bwd.cpp.o [ 16%] Building CXX object CMakeFiles/gram.dir/src/bidir_search_fwd.cpp.o [ 20%] Building CXX object CMakeFiles/gram.dir/src/skip.cpp.o [ 25%] Building CXX object CMakeFiles/gram.dir/src/bidir_search.cpp.o [ 29%] Building CXX object CMakeFiles/gram.dir/src/masks.cpp.o [ 33%] Building CXX object CMakeFiles/gram.dir/src/fm_index.cpp.o [ 37%] Building CXX object CMakeFiles/gram.dir/src/variants.cpp.o [ 41%] Building CXX object CMakeFiles/gram.dir/src/ranks.cpp.o Linking CXX static library libgram.a make[2]: warning: Clock skew detected. Your build may be incomplete. [ 41%] Built target gram Scanning dependencies of target git_version_py [ 41%] Built target git_version_py Scanning dependencies of target git_version [ 41%] Built target git_version Scanning dependencies of target gramtools make[2]: Warning: FileCMakeFiles/gramtools.dir/depend.make' has modification time 39 s in the future [ 45%] Building CXX object CMakeFiles/gramtools.dir/src/main.cpp.o In file included from /home/zam/dev/git/gramtools/src/main.cpp:11:0: /home/zam/dev/git/gramtools/include/git_version/git_version.hpp:1:1: error: stray ‘\’ in program compilation terminated due to -Wfatal-errors. make[2]: [CMakeFiles/gramtools.dir/src/main.cpp.o] Error 1 make[1]: [CMakeFiles/gramtools.dir/all] Error 2 make: *** [all] Error 2 bash-4.1$

Tried this yesterday after git pull, and today I deleted the entire dir and recloned - same issue

git log | head -n 10 commit 0e07f66751b8d46192dafd3442d9526247ad438f Author: Robyn Ffrancon rffrancon@gmail.com Date: Wed Jun 28 19:35:05 2017 +0100

stdout stored in quasimap run report.json
ffranr commented 7 years ago

From what I can tell, travis built and ran passing unit tests on this branch. Is your local system time accurate? Please see: https://stackoverflow.com/questions/3824500/compiling-c-on-remote-linux-machine-clock-skew-detected-warning

Please copy and past the contents of /home/zam/dev/git/gramtools/include/git_version/git_version.hpp

It might also help to know the versions of git, make, and cmake that you are using.

Thank you for raising an issue!

iqbal-lab commented 7 years ago

This is a new clone, hard to believe is a time issue.

cat dev/git/gramtools/include/git_version/git_version.hpp const std::string latest_commit = "0e07f66751b8d46192dafd3442d9526247ad438f";\nconst std::string current_branch = "refactor_bidir_bwd";\nconst std::string commit_log = "0e07f66 - Robyn Ffrancon, 2 hours ago : stdout stored in quasimap run report.json d2c8630 - Robyn Ffrancon, 4 hours ago : Merge branch 'py_git_version' into refactor_bidir_bwd adfde0d - Robyn Ffrancon, 4 hours ago : Merge branch 'setup_travis' into py_git_version 69bfdd2 - Robyn Ffrancon, 4 hours ago : Merge branch 'setup_travis' into refactor_bidir_bwd *****1359a11 - Robyn Ffrancon, 4 hours ago : turn off travis email notifications";

ffranr commented 7 years ago

A possible fix has been implemented on this branch: fix_git_version Please try and build from that branch.

iqbal-lab commented 7 years ago

Works for me!

ffranr commented 7 years ago

Implemented fix on all branches.