Compilation error

[ufyksb]

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]

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

[ufyksb]

Yes, just make.

[ufyksb]

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

[grenaud]

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]

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]

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]

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]

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]

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]

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

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[FabianRoger]

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

thanks for the fast answer!

[grenaud]

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!

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[FabianRoger]

of course. thanks again for the quick response