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zd1 / telseq

A software for calculating telomere length
GNU General Public License v3.0
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Bamtools Not Found #16

Closed jerryyyyy closed 6 years ago

jerryyyyy commented 6 years ago

Hello, I am having a similar error to hat has been reported for the ./configure.

I have installed Bamtools and I can see the libraries in /usr/local/include/bamtools/api.

I have tried several variants of:

xxxx@ubuntu:~/Downloads/telseq-master/src$ ./configure --with-bamtools=/usr/local/include

xxxxxxx@ubuntu:~/Downloads/telseq-master/src$ ./configure --with-bamtools=/usr/local/include checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /home/xxxxxxx/Downloads/telseq-master/src/missing: Unknown --is-lightweight' option Try/home/xxxxxxx/Downloads/telseq-master/src/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking api/BamReader.h usability... no checking api/BamReader.h presence... no checking for api/BamReader.h... no configure: error: The bamtools library must be installed (http://github.com/pezmaster31/bamtools). You can specify its path with the --with-bamtools=PATH option

Nay help appreciated!

jerryyyyy commented 6 years ago

Boy, I have tried every PATH combo in the Free World and still; cannot get this to work!

zd1 commented 6 years ago

Hi there,

Thanks for trying to use telseq. Could you try

./configure --with-bamtools=/usr/local/include/bamtools

Zhihao

jerryyyyy commented 6 years ago

Thanks for responding. Here is the full result... looks like there is something more basic at the top... XXX@ubuntu:~/Downloads/telseq-master/src$ ./configure --with-bamtools=/usr/local/include/bamtools checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /home/yesavage/Downloads/telseq-master/src/missing: Unknown --is-lightweight' option Try/home/yesavage/Downloads/telseq-master/src/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking api/BamReader.h usability... no checking api/BamReader.h presence... no checking for api/BamReader.h... no configure: error: The bamtools library must be installed (http://github.com/pezmaster31/bamtools). You can specify its path with the --with-bamtools=PATH option

zd1 commented 6 years ago

This could be due to bamtools compiled with a different compiler. Would you mind doing the following?

  1. set the env variables export CXX=/path/to/gcc/gcc-4.8.1/bin/g++ export CC=/path/to/gcc/gcc-4.8.1/bin/gcc

  2. install bamtools again (not to a system location)

  3. install telseq against the above installed bamtools

Zhihao

jerryyyyy commented 6 years ago

I think you are on to something. When I check I am using gg version 6.3.0 (Ubuntu 6.3.0-12).

The director path /usr/gin/gcc just leads to a set of links. So it is not clear how I can follow those instructions.

From: Zhihao Ding [mailto:notifications@github.com] Sent: Tuesday, October 31, 2017 8:51 AM To: zd1/telseq telseq@noreply.github.com Cc: jerryyyyy yesavage@stanford.edu; Author author@noreply.github.com Subject: Re: [zd1/telseq] Bamtools Not Found (#16)

This could be due to bamtools compiled with a different compiler. Would you mind doing the following?

  1. set the env variables export CXX=/path/to/gcc/gcc-4.8.1/bin/g++ export CC=/path/to/gcc/gcc-4.8.1/bin/gcc
  2. install bamtools again (not to a system location)
  3. install telseq against the above installed bamtools

Zhihao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zd1/telseq/issues/16#issuecomment-340807081 , or mute the thread https://github.com/notifications/unsubscribe-auth/AfoESzkhoj_kqiKKJs7Uj4dsuwgvzl44ks5sx0HwgaJpZM4QLYH0 . https://github.com/notifications/beacon/AfoES8IKgvCxTyJd2xV1ngkhWodmah-Jks5sx0HwgaJpZM4QLYH0.gif

zd1 commented 6 years ago

OK. Looks like the system compiler is found first in path. Let's try 2 and 3.

jerryyyyy commented 6 years ago

Thanks for the response.
I installed bamtools into a special directory: /programinstallers/bamtools/src/api As far as I can see all the libraries and .h files are in there. It never gets to the compilation because it never gets through the ./configure step... that is where it checks for the .h files and dies.
I have rewritten the $PATH variable multiple times as well as use the ./configure --with-bamtools=/programinstallers/bamtools/src/api (and multiple variants of this)..... We still get the same error.....:

checking for unistd.h... yes checking api/BamReader.h usability... no checking api/BamReader.h presence... no checking for api/BamReader.h... no configure: error: The bamtools library must be installed (http://github.com/pezmaster31/bamtools). You can specify its path with the --with-bamtools=PATH option