{"action":"opened","number":1871,"pull_request":{"url":"https://api.github.com/repos/biocore/qiime/pulls/1871","id":27466513,"html_url":"https://github.com/biocore/qiime/pull/1871","diff_url":"https://github.com/biocore/qiime/pull/1871.diff","patch_url":"https://github.com/biocore/qiime/pull/1871.patch","issue_url":"https://api.github.com/repos/biocore/qiime/issues/1871","number":1871,"state":"open","locked":false,"title":"ENH: status indication when installing non-Python dependencies","user":{"login":"jairideout","id":1847232,"avatar_url":"https://avatars.githubusercontent.com/u/1847232?v=3","gravatar_id":"","url":"https://api.github.com/users/jairideout","html_url":"https://github.com/jairideout","followers_url":"https://api.github.com/users/jairideout/followers","following_url":"https://api.github.com/users/jairideout/following{/other_user}","gists_url":"https://api.github.com/users/jairideout/gists{/gist_id}","starred_url":"https://api.github.com/users/jairideout/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jairideout/subscriptions","organizations_url":"https://api.github.com/users/jairideout/orgs","repos_url":"https://api.github.com/users/jairideout/repos","events_url":"https://api.github.com/users/jairideout/events{/privacy}","received_events_url":"https://api.github.com/users/jairideout/received_events","type":"User","site_admin":false},"body":"Status messages are provided while non-Python dependencies are installed via setup.py. Also fixed bug where these built dependencies would have been bundled with our source distribution.\r\n\r\nStatus output now looks like the following (updated progressively instead of dumping all text when finished):\r\n\r\n```\r\nRunning setup.py develop for qiime\r\n    Building denoiser...\r\n    Denoiser built.\r\n\r\n    Installing UCLUST...\r\n      Downloading uclust...\r\n      uclust downloaded successfully.\r\n    UCLUST installed.\r\n\r\n    Building FastTree...\r\n      Downloading FastTree.c...\r\n      FastTree.c downloaded successfully.\r\n    FastTree built.\r\n\r\n    Building SortMeRNA...\r\n      Downloading sortmerna-2.0-no-db.tar.gz...\r\n      sortmerna-2.0-no-db.tar.gz downloaded successfully.\r\n    SortMeRNA built.\r\n\r\n    Building SUMACLUST...\r\n      Downloading suma_package_V_1.0.00.tar.gz...\r\n      suma_package_V_1.0.00.tar.gz downloaded successfully.\r\n    Unable to build SUMACLUST:\r\n      stdout:\r\n        gcc -O3 -s -fopenmp -w -c -o sumaclust.o sumaclust.c -lfasta -llcs -lfile -lutils -lm\r\n        gcc -O3 -s -fopenmp -w -c -o mtcompare_sumaclust.o mtcompare_sumaclust.c -lfasta -llcs -lfile -lutils -lm\r\n        /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../libfasta\r\n        gcc -O3 -s -fopenmp -w -c -o fasta_header_parser.o fasta_header_parser.c\r\n        gcc -O3 -s -fopenmp -w -c -o fasta_seq_writer.o fasta_seq_writer.c\r\n        gcc -O3 -s -fopenmp -w -c -o fasta_header_handler.o fasta_header_handler.c\r\n        gcc -O3 -s -fopenmp -w -c -o header_mem_handler.o header_mem_handler.c\r\n        gcc -O3 -s -fopenmp -w -c -o sequence.o sequence.c\r\n        ar -cr libfasta.a fasta_header_parser.o fasta_seq_writer.o fasta_header_handler.o header_mem_handler.o sequence.o\r\n        ranlib libfasta.a\r\n        /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../liblcs\r\n        gcc -O3 -s -fopenmp -w -c -o sse_banded_LCS_alignment.o sse_banded_LCS_alignment.c\r\n        gcc -O3 -s -fopenmp -w -c -o upperband.o upperband.c\r\n        ar -cr liblcs.a sse_banded_LCS_alignment.o upperband.o\r\n        ranlib liblcs.a\r\n        /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../libfile\r\n        gcc -O3 -s -fopenmp -w -c -o fileHandling.o fileHandling.c\r\n        ar -cr libfile.a fileHandling.o\r\n        ranlib libfile.a\r\n        /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ../libutils\r\n        gcc -O3 -s -fopenmp -w -c -o utilities.o utilities.c\r\n        gcc -O3 -s -fopenmp -w -c -o debug.o debug.c\r\n        ar -cr libutils.a utilities.o debug.o\r\n        ranlib libutils.a\r\n        gcc  -o sumaclust -fopenmp sumaclust.o mtcompare_sumaclust.o -lfasta -llcs -lfile -lutils -lm  -L../libfasta -L../liblcs -L../libfile -L../libutils\r\n\r\n      stderr:\r\n        ld: library not found for -lgomp\r\n        clang: error: linker command failed with exit code 1 (use -v to see invocation)\r\n        make: *** [sumaclust] Error 1\r\n\r\n    Building swarm...\r\n      Downloading swarm-1.2.19.tar.gz...\r\n      swarm-1.2.19.tar.gz downloaded successfully.\r\n    swarm built.\r\n```\r\n\r\nFixes 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