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Compilation error #12

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ufyksb opened this issue Sep 30, 2019 · 13 comments
Open

Compilation error #12

ufyksb opened this issue Sep 30, 2019 · 13 comments

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@ufyksb
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ufyksb commented Sep 30, 2019

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
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grenaud commented Sep 30, 2019

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

@ufyksb
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ufyksb commented Sep 30, 2019

Yes, just make.

@ufyksb
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ufyksb commented Sep 30, 2019

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

@grenaud
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grenaud commented Sep 30, 2019

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
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ufyksb commented Sep 30, 2019 •
edited
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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
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grenaud commented Sep 30, 2019

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
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ufyksb commented Sep 30, 2019 •
edited
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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
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grenaud commented Sep 30, 2019

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
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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
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grenaud commented Nov 4, 2021 via email

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

thanks for the fast answer!

@grenaud
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grenaud commented Nov 4, 2021 via email

@FabianRoger
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of course. thanks again for the quick response

@allyssonallan allyssonallan mentioned this issue Jan 12, 2024
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@grenaud @FabianRoger @ufyksb