{"action":"created","issue":{"url":"https://api.github.com/repos/statnet/networkDynamic/issues/3","repository_url":"https://api.github.com/repos/statnet/networkDynamic","labels_url":"https://api.github.com/repos/statnet/networkDynamic/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/statnet/networkDynamic/issues/3/comments","events_url":"https://api.github.com/repos/statnet/networkDynamic/issues/3/events","html_url":"https://github.com/statnet/networkDynamic/issues/3","id":530775909,"node_id":"MDU6SXNzdWU1MzA3NzU5MDk=","number":3,"title":"CRAN warning about gcc install error","user":{"login":"skyebend","id":3160937,"node_id":"MDQ6VXNlcjMxNjA5Mzc=","avatar_url":"https://avatars3.githubusercontent.com/u/3160937?v=4","gravatar_id":"","url":"https://api.github.com/users/skyebend","html_url":"https://github.com/skyebend","followers_url":"https://api.github.com/users/skyebend/followers","following_url":"https://api.github.com/users/skyebend/following{/other_user}","gists_url":"https://api.github.com/users/skyebend/gists{/gist_id}","starred_url":"https://api.github.com/users/skyebend/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/skyebend/subscriptions","organizations_url":"https://api.github.com/users/skyebend/orgs","repos_url":"https://api.github.com/users/skyebend/repos","events_url":"https://api.github.com/users/skyebend/events{/privacy}","received_events_url":"https://api.github.com/users/skyebend/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2019-12-01T18:47:35Z","updated_at":"2019-12-02T02:53:15Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Email from Ripley:\r\nThis concerns packages\r\n\r\n<lots of packages> ... latentnet ... msm networkDynamic ...\r\n\r\nwhich fail to install with gcc trunk which is due to be released as gcc \r\n10.0.x early in 2020.  It defaults to -fno-common, which stricter on \r\nsome multiply-defined symbols -- see §1.6.4.1 of 'Writing R Extensions' \r\nin current R-devel.\r\n\r\nSee https://www.stats.ox.ac.uk/pub/bdr/gcc10/ for the logs, which will \r\nbe linked from the CRAN results page under 'Additional issues'.\r\n\r\nWe expect the issues to also be seen when compiling with earlier \r\nversions of gcc using the (non-default) flag -fno-common: this has been \r\nconfirmed for gcc 9 on Linux, and also for clang on macOS.\r\n\r\nPlease correct as soon as possible and before Jan 10 to safely retain on \r\nCRAN.  (This is after the CRAN shutdown from Dec 20 to Jan 6.)\r\n\r\n```\r\n* installing *source* package ‘networkDynamic’ ...\r\n** package ‘networkDynamic’ successfully unpacked and MD5 sums checked\r\n** using staged installation\r\n** libs\r\nmake[2]: Entering directory '/data/gannet/ripley/R/packages/tests-gcc10/networkDynamic/src'\r\n/usr/local/gcc10/bin/gcc -I\"/data/gannet/ripley/R/R-gcc10/include\" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/network/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c Rinit.c -o Rinit.o\r\n/usr/local/gcc10/bin/gcc -I\"/data/gannet/ripley/R/R-gcc10/include\" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/network/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c diagnostics.c -o diagnostics.o\r\n/usr/local/gcc10/bin/gcc -I\"/data/gannet/ripley/R/R-gcc10/include\" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/network/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c edgetree.c -o edgetree.o\r\n/usr/local/gcc10/bin/gcc -I\"/data/gannet/ripley/R/R-gcc10/include\" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/network/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c infection.c -o infection.o\r\n/usr/local/gcc10/bin/gcc -I\"/data/gannet/ripley/R/R-gcc10/include\" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/network/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c is.active.c -o is.active.o\r\n/usr/local/gcc10/bin/gcc -I\"/data/gannet/ripley/R/R-gcc10/include\" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/network/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c spellfunctions.c -o spellfunctions.o\r\n/usr/local/gcc10/bin/gcc -I\"/data/gannet/ripley/R/R-gcc10/include\" -DNDEBUG  -I'/data/gannet/ripley/R/test-3.7/network/include' -I/usr/local/include   -fpic  -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection  -c wtedgetree.c -o wtedgetree.o\r\n/usr/local/gcc10/bin/gcc -shared -L/usr/local/gcc10/lib64 -L/usr/local/lib64 -o networkDynamic.so Rinit.o diagnostics.o edgetree.o infection.o is.active.o spellfunctions.o wtedgetree.o\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:7: multiple definition of `getListElement'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:7: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:8: multiple definition of `setListElement'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:8: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:34: multiple definition of `netSetVertexAttrib_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:34: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:33: multiple definition of `netSetNetAttrib_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:33: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:32: multiple definition of `netDelVertexAttrib_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:32: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:31: multiple definition of `netDelNetAttrib_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:31: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:30: multiple definition of `netDelEdgeAttrib_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:30: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:29: multiple definition of `netAddEdges_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:29: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:28: multiple definition of `netAddEdge_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:28: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:25: multiple definition of `netNetSize_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:25: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:24: multiple definition of `netNetEdgecount_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:24: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:23: multiple definition of `netIsNetwork_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:23: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:22: multiple definition of `netIsMulti_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:22: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:21: multiple definition of `netIsLoop_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:21: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:20: multiple definition of `netIsHyper_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:20: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:19: multiple definition of `netIsDir_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:19: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:18: multiple definition of `netIsAdj_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:18: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:17: multiple definition of `netHasLoops_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:17: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:16: multiple definition of `netGetNetAttrib_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:16: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:15: multiple definition of `netGetNeighborhood_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:15: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:14: multiple definition of `netGetEdges_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:14: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:13: multiple definition of `netGetEdgeIDs_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:13: first defined here\r\n/usr/bin/ld: spellfunctions.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:12: multiple definition of `netGetEdgeAttrib_ptr'; Rinit.o:/data/gannet/ripley/R/test-3.7/network/include/network.h:12: first defined here\r\ncollect2: error: ld returned 1 exit status\r\nmake[2]: *** [/data/gannet/ripley/R/R-gcc10/share/make/shlib.mk:6: networkDynamic.so] Error 1\r\nmake[2]: Target 'all' not remade because of errors.\r\nmake[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-gcc10/networkDynamic/src'\r\nERROR: compilation failed for package ‘networkDynamic’\r\n* removing ‘/data/gannet/ripley/R/packages/tests-gcc10/networkDynamic.Rcheck/networkDynamic’\r\n```\r\nSeems like some kind of repetition of the C-level api headers? \r\n@chad-klumb have you seen this with other packages?, not sure I have C experience to resolve\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/statnet/networkDynamic/issues/comments/560205759","html_url":"https://github.com/statnet/networkDynamic/issues/3#issuecomment-560205759","issue_url":"https://api.github.com/repos/statnet/networkDynamic/issues/3","id":560205759,"node_id":"MDEyOklzc3VlQ29tbWVudDU2MDIwNTc1OQ==","user":{"login":"chad-klumb","id":10733914,"node_id":"MDQ6VXNlcjEwNzMzOTE0","avatar_url":"https://avatars2.githubusercontent.com/u/10733914?v=4","gravatar_id":"","url":"https://api.github.com/users/chad-klumb","html_url":"https://github.com/chad-klumb","followers_url":"https://api.github.com/users/chad-klumb/followers","following_url":"https://api.github.com/users/chad-klumb/following{/other_user}","gists_url":"https://api.github.com/users/chad-klumb/gists{/gist_id}","starred_url":"https://api.github.com/users/chad-klumb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chad-klumb/subscriptions","organizations_url":"https://api.github.com/users/chad-klumb/orgs","repos_url":"https://api.github.com/users/chad-klumb/repos","events_url":"https://api.github.com/users/chad-klumb/events{/privacy}","received_events_url":"https://api.github.com/users/chad-klumb/received_events","type":"User","site_admin":false},"created_at":"2019-12-02T02:53:15Z","updated_at":"2019-12-02T02:53:15Z","author_association":"NONE","body":"Merging `Rinit.c` and `spellfunctions.c` into a single file appears to work.  (very ugly, of course)"}}
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