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rrwick / Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
http://rrwick.github.io/Bandage/
GNU General Public License v3.0
578 stars 96 forks source link

install error #98

Open huilin-al opened 3 years ago

huilin-al commented 3 years ago

/usr/include/c++/9/cstdlib:75:15: fatal error: stdlib.h: 没有那个文件或目录 75 | #include_next | ^~~~~~ compilation terminated. make: *** [Makefile:1234：main.o] 错误 1

drelo commented 3 years ago

Hi, I am using Fedora and Qt and I got the same error. Any way to handle this? Thanks.

huilin-al commented 3 years ago

Hi,This is due to the fact that gcc7 has been included in the libstdc .h for better optimization, C Library's header file stdlib.h uses Include_next, and include_next is sensitive to the gcc system header file path. Solve:Add the following next line to the bandage.pro file QMAKE_CFLAGS_ISYSTEM -I.

drelo commented 3 years ago

Thanks, I added it as the last line [I don't know if this is correct] but then Qt throws this error

11:48:56: Starting: "/home/andrespara/anaconda3/bin/qmake" /home/andrespara/andres/pangenomas/BANDAGE/DIR/Bandage/Bandage.pro -spec linux-g++ /home/andrespara/andres/pangenomas/BANDAGE/DIR/Bandage/Bandage.pro:274: Extra characters after test expression. Error processing project file: /home/andrespara/andres/pangenomas/BANDAGE/DIR/Bandage/Bandage.pro 11:48:56: The process "/home/andrespara/anaconda3/bin/qmake" exited with code 3. Error while building/deploying project Bandage (kit: Desktop) When executing step "qmake" 11:48:56: Elapsed time: 00:00.

The Issue is 'Extra characters after test expression'

If I ask to show in editor the error it points to the extra line

Is there anything extra to do? Thanks again

El jue., 24 sept. 2020 a las 23:22, huilin-al (notifications@github.com) escribió:

Hi,This is due to the fact that gcc7 has been included in the libstdc .h for better optimization, C Library's header file stdlib.h uses Include_next, and include_next is sensitive to the gcc system header file path. Solve:Add the following next line to the bandage.pro file QMAKE_CFLAGS_ISYSTEM -I.

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huilin-al commented 3 years ago

Can you show me all your installation steps so that I know which step you take is different from mine, and my bandage can compile normally by additioning a line.

drelo commented 3 years ago

Thanks for your help. Sorry for the late reply I didn't have access to this machine and the graphical interface during the weekend, I am using Qt Creator 4.13.1 and I used git clone https://github.com/rrwick/Bandage.git to download Bandage, I edited the .pro file as in the attachment [I just changed the extension] and then I opened the Qt software and I noticed the same info 'Extra characters after text expression'

I am using Fedora 32. Let me know any additional details needed for this.

Bandage.pro.txt

The Qt editor highlights the extra line How can I fix this?

bandage

huilin-al commented 3 years ago

hi,I installed it like this sudo apt-get update sudo apt-get install build-essential git qtbase5-dev libqt5svg5-dev git clone https://github.com/rrwick/Bandage.git export QT_SELECT=5 qmake make In the bandage.pro file, add the following line QMAKE_CFLAGS_ISYSTEM = -I sudo make install Bandage --help I don't know if I can help you

AdamVS commented 3 years ago

adding the line (below) to the bandage.pro file works for me to correct the stdlib.h fatal error (in Ubuntu 18.04) QMAKE_CFLAGS_ISYSTEM = -I

matthewstuartedwards commented 3 years ago

I was having the stdlib.h No such file error as well.

For me, commenting the unix:INCLUDEPATH += /usr/include/ from the Bandage.pro file fixed the problem for me. Re-run qmake after making the change, then make.