payload: {"action":"opened","issue":{"url":"https://api.github.com/repos/Gaius-Augustus/Augustus/issues/50","repository_url":"https://api.github.com/repos/Gaius-Augustus/Augustus","labels_url":"https://api.github.com/repos/Gaius-Augustus/Augustus/issues/50/labels{/name}","comments_url":"https://api.github.com/repos/Gaius-Augustus/Augustus/issues/50/comments","events_url":"https://api.github.com/repos/Gaius-Augustus/Augustus/issues/50/events","html_url":"https://github.com/Gaius-Augustus/Augustus/issues/50","id":426966405,"node_id":"MDU6SXNzdWU0MjY5NjY0MDU=","number":50,"title":"augustus-3.3.2: /bin/sh: line 0: cd: ../bin: No such file or directory","user":{"login":"mmokrejs","id":3297852,"node_id":"MDQ6VXNlcjMyOTc4NTI=","avatar_url":"https://avatars1.githubusercontent.com/u/3297852?v=4","gravatar_id":"","url":"https://api.github.com/users/mmokrejs","html_url":"https://github.com/mmokrejs","followers_url":"https://api.github.com/users/mmokrejs/followers","following_url":"https://api.github.com/users/mmokrejs/following{/other_user}","gists_url":"https://api.github.com/users/mmokrejs/gists{/gist_id}","starred_url":"https://api.github.com/users/mmokrejs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmokrejs/subscriptions","organizations_url":"https://api.github.com/users/mmokrejs/orgs","repos_url":"https://api.github.com/users/mmokrejs/repos","events_url":"https://api.github.com/users/mmokrejs/events{/privacy}","received_events_url":"https://api.github.com/users/mmokrejs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2019-03-29T12:37:21Z","updated_at":"2019-03-29T12:37:21Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n  it seems the `Makefile` has some wrong expectations of directory structure.\r\n\r\n```\r\n...\r\ncd homGeneMapping; make clean;\r\nmake[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping'\r\nmake[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.\r\n(cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping)\r\nmake[3]: Entering directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping/src'\r\nrm -f homGeneMapping gene.o genome.o\r\nmake[3]: Leaving directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping/src'\r\n/bin/sh: line 0: cd: ../bin: No such file or directory\r\n/bin/sh: line 0: cd: ../../../bin: No such file or directory\r\nmake[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping'\r\ncd joingenes; make clean;\r\nmake[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/joingenes'\r\n...\r\n```\r\n\r\nLuckily, it is re-entered later:\r\n\r\n```\r\ncd homGeneMapping; make;\r\nmake[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping'\r\nmake[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.\r\n(cd src; make)\r\nmake[3]: Entering directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping/src'\r\ng++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize  -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize  -Wl,-O1 -Wl,--as-needed -o gene.o gene.cc -I../include\r\ng++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize  -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize  -Wl,-O1 -Wl,--as-needed -o genome.o genome.cc -I../include\r\ng++ -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize   -o homGeneMapping main.cc gene.o genome.o -I../include  \r\ncp homGeneMapping ../../../bin/homGeneMapping\r\nmake[3]: Leaving directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping/src'\r\nmake[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/augustus-3.3.2/work/Augustus-3.3.2/auxprogs/homGeneMapping'\r\ncd joingenes; make;\r\n```\r\n\r\nUse `cp -p` instead of `cp homGeneMapping ../../../bin/homGeneMapping` or even better, use `g++ -o ../../../bin/homGeneMapping` directly like in other cases through the project."}}
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