Summary: | sci-chemistry/rasmol-2.7.5.2 with sci-libs/cbflib-0.9.3.3 - cc1: fatal error: /usr/include/cbflib/stdc-predef.h: Permission denied | ||
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Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
Component: | Current packages | Assignee: | Gentoo Chemistry-Related Packages <sci-chemistry> |
Status: | RESOLVED WORKSFORME | ||
Severity: | normal | ||
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
build.log
/var/tmp/portage/sci-libs/cbflib-0.9.3.3/temp/build.log |
Description
Juergen Rose
2013-12-08 23:45:23 UTC
Created attachment 364968 [details]
build.log
cc1: fatal error: /usr/include/cbflib/stdc-predef.h: Permission denied This is the actual error. Why can't that file be read? (In reply to Jeroen Roovers from comment #2) > cc1: fatal error: /usr/include/cbflib/stdc-predef.h: Permission denied > > This is the actual error. Why can't that file be read? Because this file does not exist anymore: rose@leopard:/home_leopard/rose(4)$ qlist -Iv cbflib sci-libs/cbflib-0.9.3.3 rose@leopard:/home_leopard/rose(5)$ qlist -Iv cbflib | grep stdc-predef This error is unreproducible here. I would rather guess it is from cbflib. Could you please attach a build.log from cbflib? or something completely unrelated. I don't have any clue here. I can't reproduce this either. cbflib-0.9.2.4 does not have the file /usr/include/cbflib/stdc-predef.h. Could that header file be pulled in by a library other than cbflib? (In reply to Justin Lecher from comment #4) > This error is unreproducible here. I would rather guess it is from cbflib. > Could you please attach a build.log from cbflib? I just recompiled cbflib. I will attach the build.log/ Created attachment 365997 [details]
/var/tmp/portage/sci-libs/cbflib-0.9.3.3/temp/build.log
But also after recompiling cbflib, 'emerge rasmol' fails with the same error. BTW., I was searching for stdc-predef.h in all files of the rasmol tree, and could it only find in build.log: root@lynx:/root(18)# find /var/tmp/portage/sci-chemistry/rasmol-2.7.5.2/ -type f -exec grep stdc-predef.h {} \; -print cc1: fatal error: /usr/include/cbflib/stdc-predef.h: Permission denied /var/tmp/portage/sci-chemistry/rasmol-2.7.5.2/temp/build.log Then I was searching for stdc-predef.h under /usr/include: root@lynx:/root(19)# find /usr/include/ -type f -exec grep stdc-predef.h {} \; -print #include <stdc-predef.h> /usr/include/features.h root@lynx:/root(20)# ll /usr/include/features.h -rw-r--r-- 1 root root 13141 Jun 26 13:47 /usr/include/features.h root@lynx:/root(21)# qfile -v /usr/include/features.h sys-libs/glibc-2.17 (/usr/include/features.h) The error happens here only at one system. And I can not find differences in the environment settings between this and the other systems, which should be relevant to rasmol. Any idea? I really have no clue here Which libtool version are you using? @toolchain, do you have any clue what is going on here? glibc installs both /usr/include/features.h and /usr/include/stdc-predef.h. this is to be expected. make sure the permissions on the dir /usr/include/cbflib/ aren't broken. (In reply to Justin Lecher from comment #12) > Which libtool version are you using? rose@lynx:/home/rose(2)$ qlist -Iv libtool sys-devel/libtool-2.4.2 I cannot help here. There must be something wrong on your side. (In reply to SpanKY from comment #14) > glibc installs both /usr/include/features.h and /usr/include/stdc-predef.h. > this is to be expected. > > make sure the permissions on the dir /usr/include/cbflib/ aren't broken. At the affected system I had: rose@lynx:/home/rose(3)$ ll -d /usr/include/cbflib drw-r--r-- 2 root root 4096 23. Dez 16:59 /usr/include/cbflib/ at an other system I have: root@impala:/root(10)# ll -d /usr/include/cbflib drwxr-xr-x 2 root root 4096 Dec 7 10:45 /usr/include/cbflib/ After adding the search permission to /usr/include/cbflib I could again emerge rasmol. So closing this now as we will not be able to figure out how the permission changes happened. Thanks Mike for the final clue. Now I have the next system, where /usr/include/cbflib is not searchable: root@tiger:/root(8)# ll -d /usr/include/cbflib drw-r--r-- 2 root root 4096 Dec 20 06:59 /usr/include/cbflib/ I suppose, that I did not manually remove the search permission for g and o. bad perms on a dir in /usr/include isn't really the domain of toolchain, so i'll let the respective maintainers sort things out I have no clue what triggers this bad permissions. |