Compilation error #12

ufyksb · 2019-09-30T11:40:19Z

While running make I get the following error:
g++ -Wall -lm -O3 -I. -Igzstream/ -I/home/users/xxx/deML-master/bamtools/build/src/api/include/ -I/home/users/xxx/deML-master/bamtools/build/src/include/ -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o
In file included from ReconsReferenceBAM.cpp:8:0:
ReconsReferenceBAM.h:14:10: fatal error: api/BamMultiReader.h: No such file or directory
#include "api/BamMultiReader.h"
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:45: recipe for target 'ReconsReferenceBAM.o' failed
make[1]: *** [ReconsReferenceBAM.o] Error 1

grenaud · 2019-09-30T11:44:03Z

just to be sure, did you type make without -j #? like just make?

ufyksb · 2019-09-30T12:41:04Z

Yes, just make.

ufyksb · 2019-09-30T12:47:49Z

Also: BamMultiReader.h is being created in deML-master/bamtools/src/api

grenaud · 2019-09-30T12:49:30Z

could you make sure you have cmake3, go the deML main directory and type:
rm -rfv bamtools/
and type:
cd bamtools/ && mkdir -p build/ && cd build/ && cmake .. && make && cd ../..

could you post the output?

ufyksb · 2019-09-30T12:59:22Z

cd bamtools/ && mkdir -p build/ && cd build/ && cmake .. && make && cd ../..
CMake Error: The source directory "/home/xxx/Programy/deML-master/bamtools" does not appear to contain CMakeLists.txt.

grenaud · 2019-09-30T13:01:26Z

sorry! my bad:
rm -rfv bamtools/
git clone --recursive https://github.com/pezmaster31/bamtools.git
cd bamtools/ && mkdir -p build/ && cd build/ && cmake .. && make && cd ../..

ufyksb · 2019-09-30T13:14:12Z

I've managed to compile bamtools:
cd bamtools/ && mkdir -p build/ && cd build/ && cmake .. && make && cd ../..
(...)
[100%] Built target bamtools_cmd

Calling make in deML-master still generates an error:
make
rm -rf SimpleJSON/
git clone --recursive https://github.com/MJPA/SimpleJSON.git
Cloning into 'SimpleJSON'...
remote: Enumerating objects: 325, done.
remote: Total 325 (delta 0), reused 0 (delta 0), pack-reused 325
Receiving objects: 100% (325/325), 77.22 KiB | 617.00 KiB/s, done.
Resolving deltas: 100% (162/162), done.
make -C SimpleJSON
make[1]: Entering directory '/home/users/xxx/deML-master/SimpleJSON'
g++ -c -Wall src/JSON.cpp -o obj/JSON.o
g++ -c -Wall src/JSONValue.cpp -o obj/JSONValue.o
g++ -c -Wall src/demo/nix-main.cpp -o obj/demo/nix-main.o
g++ -c -Wall src/demo/example.cpp -o obj/demo/example.o
g++ -c -Wall src/demo/testcases.cpp -o obj/demo/testcases.o
g++ -lm obj/JSON.o obj/JSONValue.o obj/demo/nix-main.o obj/demo/example.o obj/demo/testcases.o -o JSONDemo
make[1]: Leaving directory '/home/users/xxx/deML-master/SimpleJSON'
make -C libgab
make[1]: Entering directory '/home/users/xxx/deML-master/libgab'
g++ -Wall -lm -O3 -I. -Igzstream/ -I/home/users/xxx/deML-master/bamtools/build/src/api/include/ -I/home/xxx/Programy/deML-master/bamtools/build/src/include/ -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o
In file included from ReconsReferenceBAM.cpp:8:0:
ReconsReferenceBAM.h:14:10: fatal error: api/BamMultiReader.h: No such file or directory
#include "api/BamMultiReader.h"
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:45: recipe for target 'ReconsReferenceBAM.o' failed
make[1]: *** [ReconsReferenceBAM.o] Error 1
make[1]: Leaving directory '/home/xxx/Programy/deML-master/libgab'
Makefile:24: recipe for target 'libgab/utils.o' failed
make: *** [libgab/utils.o] Error 2

grenaud · 2019-09-30T14:18:23Z

Thank you for aprising me!! The people at bamtools decided to do a little create rearrangement of the directories. This is so annoying...

Anyway, I added a checkout of a specific bamtools version. I have stopped using this library. I now need to expunge bamtools from all my programs.

delete deML and redo a git clone https://github.com/grenaud/deml.git
Thank you again!

FabianRoger · 2021-11-04T13:49:28Z

Hi,

I am on a MacbookPro 13 "" M1 running MacOS BigSour. I have tried to install deML but it fails. I have cmake installed. The full error I get is:

rm -rf libgab/
git clone --recursive https://github.com/grenaud/libgab.git
Cloning into 'libgab'...
remote: Enumerating objects: 382, done.
remote: Counting objects: 100% (11/11), done.
remote: Compressing objects: 100% (9/9), done.
remote: Total 382 (delta 4), reused 7 (delta 2), pack-reused 371
Receiving objects: 100% (382/382), 136.57 KiB | 822.00 KiB/s, done.
Resolving deltas: 100% (234/234), done.
make -C libgab
Makefile:72: warning: overriding commands for target `-'
Makefile:68: warning: ignoring old commands for target `-'
bamtools found
Makefile:72: warning: overriding commands for target `-'
Makefile:68: warning: ignoring old commands for target `-'
c++ -Wall  -lm -O3 -I. -Igzstream/ -I/Users/fabian/Downloads/deML/bamtools/src/ -I/Users/fabian/Downloads/deML/bamtools/src/  -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o
clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument]
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:58:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:105:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:417:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:37:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:58:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:105:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:418:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:58:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:121:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:60:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:642:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/utility:205:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:668:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/typeinfo:60:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:671:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:93:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:674:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:423:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:677:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:154:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:681:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/atomic:576:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__threading_support:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/chrono:831:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:681:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/atomic:581:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:683:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:644:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:507:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:648:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:11:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:285:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:14:
In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/map:482:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__node_handle:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/optional:158:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:14:
In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/map:489:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:14:
In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/sstream:173:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:138:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:215:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:181:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
In file included from ReconsReferenceBAM.cpp:8:
In file included from ./ReconsReferenceBAM.h:14:
In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/sstream:173:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:138:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:215:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:519:
gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [ReconsReferenceBAM.o] Error 1
make[1]: *** [/Users/fabian/Downloads/deML/bamtools/src/-/Users/fabian/Downloads/deML/bamtools/src] Error 2
make: *** [libgab/libgab.a] Error 2

grenaud · 2021-11-04T13:52:01Z

Hi Fabian, Can you try installing on a Unix cluster and accessing it via your laptop?

…

On Thu, Nov 4, 2021 at 2:49 PM FabianRoger ***@***.***> wrote: Hi, I am on a MacbookPro 13 "" M1 running MacOS BigSour. I have tried to install deML but it fails. I have cmake installed. The full error I get is: rm -rf libgab/ git clone --recursive https://github.com/grenaud/libgab.git Cloning into 'libgab'... remote: Enumerating objects: 382, done. remote: Counting objects: 100% (11/11), done. remote: Compressing objects: 100% (9/9), done. remote: Total 382 (delta 4), reused 7 (delta 2), pack-reused 371 Receiving objects: 100% (382/382), 136.57 KiB | 822.00 KiB/s, done. Resolving deltas: 100% (234/234), done. make -C libgab Makefile:72: warning: overriding commands for target `-' Makefile:68: warning: ignoring old commands for target `-' bamtools found Makefile:72: warning: overriding commands for target `-' Makefile:68: warning: ignoring old commands for target `-' c++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/fabian/Downloads/deML/bamtools/src/ -I/Users/fabian/Downloads/deML/bamtools/src/ -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:58: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:105: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:417: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:37: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:58: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:105: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:418: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:58: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:121: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/bit:60: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:642: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/utility:205: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:668: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/typeinfo:60: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:671: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:93: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:674: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iterator:423: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:677: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:154: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:681: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/atomic:576: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__threading_support:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/chrono:831: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:681: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/atomic:581: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:683: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:644: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:507: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:276: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__bit_reference:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:648: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:11: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:285: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:14: In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:13: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/map:482: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__node_handle:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/optional:158: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:14: In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:13: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/map:489: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:14: In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/sstream:173: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:138: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:181: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ In file included from ReconsReferenceBAM.cpp:8: In file included from ./ReconsReferenceBAM.h:14: In file included from /Users/fabian/Downloads/deML/bamtools/src/api/BamMultiReader.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/sstream:173: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ostream:138: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:519: gzstream/version:1:1: error: expected unqualified-id 1.5 (08 Jan 2003) ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[2]: *** [ReconsReferenceBAM.o] Error 1 make[1]: *** [/Users/fabian/Downloads/deML/bamtools/src/-/Users/fabian/Downloads/deML/bamtools/src] Error 2 make: *** [libgab/libgab.a] Error 2 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQRNI2KY2XQNVQTUQY2ZXLUKKFPHANCNFSM4I3ZW22Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

FabianRoger · 2021-11-04T13:56:10Z

unfortunately that's not an option right now. Does this mean it wont work on my laptop?

thanks for the fast answer!

grenaud · 2021-11-04T14:00:09Z

It could but I don't have time currently to fix it. tor. d. 4. nov. 2021 2.56 PM skrev FabianRoger ***@***.***>:

…

unfortunately that's not an option right now. Does this mean it wont work on my laptop? thanks for the fast answer! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQRNIZAI447G6J2RVUCMLDUKKGIJANCNFSM4I3ZW22Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

FabianRoger · 2021-11-04T14:17:23Z

of course. thanks again for the quick response

allyssonallan mentioned this issue Jan 12, 2024

ARM-64 / OS-64 issues grenaud/gargammel#20

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Compilation error #12

Compilation error #12

ufyksb commented Sep 30, 2019

grenaud commented Sep 30, 2019

ufyksb commented Sep 30, 2019

ufyksb commented Sep 30, 2019

grenaud commented Sep 30, 2019

ufyksb commented Sep 30, 2019 •

edited

Loading

grenaud commented Sep 30, 2019

ufyksb commented Sep 30, 2019 •

edited

Loading

grenaud commented Sep 30, 2019

FabianRoger commented Nov 4, 2021

grenaud commented Nov 4, 2021 via email

FabianRoger commented Nov 4, 2021

grenaud commented Nov 4, 2021 via email

FabianRoger commented Nov 4, 2021

Compilation error #12

Compilation error #12

Comments

ufyksb commented Sep 30, 2019

grenaud commented Sep 30, 2019

ufyksb commented Sep 30, 2019

ufyksb commented Sep 30, 2019

grenaud commented Sep 30, 2019

ufyksb commented Sep 30, 2019 • edited Loading

grenaud commented Sep 30, 2019

ufyksb commented Sep 30, 2019 • edited Loading

grenaud commented Sep 30, 2019

FabianRoger commented Nov 4, 2021

grenaud commented Nov 4, 2021 via email

FabianRoger commented Nov 4, 2021

grenaud commented Nov 4, 2021 via email

FabianRoger commented Nov 4, 2021

ufyksb commented Sep 30, 2019 •

edited

Loading

ufyksb commented Sep 30, 2019 •

edited

Loading