https://github.com/fomightez/bioptools-binder
bioptools available in Jupyter session served via myBinder.org
https://github.com/fomightez/bioptools-binder
Last synced: 4 months ago
JSON representation
bioptools available in Jupyter session served via myBinder.org
- Host: GitHub
- URL: https://github.com/fomightez/bioptools-binder
- Owner: fomightez
- Created: 2022-04-05T19:05:06.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2022-04-05T19:39:09.000Z (about 3 years ago)
- Last Synced: 2024-12-28T13:25:52.957Z (5 months ago)
- Language: Shell
- Size: 2.93 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# bioptools-binder
bioptools available in Jupyter session served via myBinder.org
[](https://mybinder.org/v2/gh/fomightez/bioptools-binder/main)
FAILS CURRENTLY TO RUN VIA MYBINDER
------------------------------------
**Won't build in current state.**
Fails in build now at current end of `make` step with same errors (`error: C++ style comments are not allowed in ISO C90`) as when I tried installing inside a running session:
```text
gcc -fPIC -ansi -Wall -pedantic -g -DGUNZIP_SUPPORT -finline-functions -D XML_SUPPORT -I/srv/conda/include/libxml2 -I/srv/conda/include -o ReadPDB.o -c ReadPDB.c
In file included from /srv/conda/include/libxml2/libxml/encoding.h:31:0,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/ucnv.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/ucnv.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/ucnv.h:52:0,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/ucnv_err.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/ucnv_err.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/ucnv_err.h:88:0,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utypes.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/utypes.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utypes.h:38:0,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/umachine.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/umachine.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/umachine.h:46:0,
from /srv/conda/include/unicode/utypes.h:38,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/ptypes.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/ptypes.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/ptypes.h:52:0,
from /srv/conda/include/unicode/umachine.h:46,
from /srv/conda/include/unicode/utypes.h:38,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/platform.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/platform.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/platform.h:24:0,
from /srv/conda/include/unicode/ptypes.h:52,
from /srv/conda/include/unicode/umachine.h:46,
from /srv/conda/include/unicode/utypes.h:38,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/uconfig.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/uconfig.h:1:1: error: (this will be reported only once per input file)
/srv/conda/include/unicode/uconfig.h:456:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // __UCONFIG_H__
^
In file included from /srv/conda/include/unicode/platform.h:25:0,
from /srv/conda/include/unicode/ptypes.h:52,
from /srv/conda/include/unicode/umachine.h:46,
from /srv/conda/include/unicode/utypes.h:38,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/uvernum.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/uvernum.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/ptypes.h:52:0,
from /srv/conda/include/unicode/umachine.h:46,
from /srv/conda/include/unicode/utypes.h:38,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/platform.h:885:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // _PLATFORM_H
^
In file included from /srv/conda/include/unicode/utypes.h:38:0,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/umachine.h:313:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_DEFINE_FALSE_AND_TRUE
^
In file included from /srv/conda/include/unicode/umachine.h:489:0,
from /srv/conda/include/unicode/utypes.h:38,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/urename.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/urename.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utypes.h:39:0,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/uversion.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/uversion.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utypes.h:44:0,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utf.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/utf.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utf.h:217:0,
from /srv/conda/include/unicode/utypes.h:44,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utf8.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/utf8.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utf.h:218:0,
from /srv/conda/include/unicode/utypes.h:44,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utf16.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/utf16.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utf.h:221:0,
from /srv/conda/include/unicode/utypes.h:44,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utf_old.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/utf_old.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utf_old.h:145:0,
from /srv/conda/include/unicode/utf.h:221,
from /srv/conda/include/unicode/utypes.h:44,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utf.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/utf.h:1:1: error: (this will be reported only once per input file)
In file included from /srv/conda/include/unicode/utf.h:221:0,
from /srv/conda/include/unicode/utypes.h:44,
from /srv/conda/include/unicode/ucnv_err.h:88,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utf_old.h:1199:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // !U_HIDE_DEPRECATED_API && !U_HIDE_OBSOLETE_UTF_OLD_H
^
In file included from /srv/conda/include/unicode/ucnv_err.h:88:0,
from /srv/conda/include/unicode/ucnv.h:52,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/utypes.h:447:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:491:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DRAFT_API
^
/srv/conda/include/unicode/utypes.h:499:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:546:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:579:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:605:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:641:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:662:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:682:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
/srv/conda/include/unicode/utypes.h:690:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
In file included from /srv/conda/include/unicode/ucnv.h:53:0,
from /srv/conda/include/libxml2/libxml/encoding.h:31,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/uenum.h:1:1: error: C++ style comments are not allowed in ISO C90
// © 2016 and later: Unicode, Inc. and others.
^
/srv/conda/include/unicode/uenum.h:1:1: error: (this will be reported only once per input file)
/srv/conda/include/unicode/uenum.h:30:10: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_SHOW_CPLUSPLUS_API
^
In file included from /srv/conda/include/libxml2/libxml/encoding.h:31:0,
from /srv/conda/include/libxml2/libxml/parser.h:812,
from ReadPDB.c:325:
/srv/conda/include/unicode/ucnv.h:57:10: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_SHOW_CPLUSPLUS_API
^
/srv/conda/include/unicode/ucnv.h:954:9: warning: extra tokens at end of #endif directive [-Wendif-labels]
#endif // U_HIDE_DEPRECATED_API
^
Makefile:126: recipe for target 'ReadPDB.o' failed
make[1]: Leaving directory '/home/jovyan/bioptools/bioptools-1.10/src/libsrc/bioplib/src'
make[1]: *** [ReadPDB.o] Error 1
make: *** [bioplib] Error 2
Makefile:16: recipe for target 'bioplib' failed
Removing intermediate container 350e6ffdffad
The command '/bin/sh -c ./postBuild' returned a non-zero code: 2Built image, launching...
Failed to connect to event stream
```
I cannot see how advice from [here](https://github.com/ACRMGroup/bioptools/issues/14) could be used to make this work via MyBinder.