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biosails / pheniqs

Fast and accurate sequence demultiplexing
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error while installing pheniqs under centos 6 using ppkg.py #14

Closed nizardrou closed 6 years ago

nizardrou commented 6 years ago

Tried to install pheniqs under centos 6 using the ppkg.py script but it exited with a CRITICAL ERROR,

`./tool/ppkg.py build build/trunk_static.json DEBUG:Pipeline:loading /home/nd48/pheniqs-master/build/trunk_static.json DEBUG:Pipeline:creating directory /home/nd48/pheniqs-master/bin/trunk_static DEBUG:Pipeline:creating directory /home/nd48/pheniqs-master/bin/trunk_static/install DEBUG:Pipeline:creating directory /home/nd48/pheniqs-master/bin/trunk_static/package INFO:Package:unpacking zlib 1.2.11 INFO:Package:configuring make environment zlib 1.2.11 DEBUG:Package:./configure --prefix=/home/nd48/pheniqs-master/bin/trunk_static/install INFO:Package:building with make zlib 1.2.11 DEBUG:Package:make INFO:Package:installing with make zlib 1.2.11 DEBUG:Package:make install INFO:Package:unpacking bz2 1.0.6 INFO:Package:building bz2 1.0.6 dynamic library DEBUG:Package:make --file Makefile-libbz2_so PREFIX=/home/nd48/pheniqs-master/bin/trunk_static/install DEBUG:Package:copying /home/nd48/pheniqs-master/bin/trunk_static/package/bzip2-1.0.6/libbz2.so.1.0.6 to /home/nd48/pheniqs-master/bin/trunk_static/install/lib/libbz2.so.1.0.6 INFO:Package:symlinking libbz2.so.1.0.6 to /home/nd48/pheniqs-master/bin/trunk_static/install/lib/libbz2.so.1.0 INFO:Package:symlinking libbz2.so.1.0.6 to /home/nd48/pheniqs-master/bin/trunk_static/install/lib/libbz2.so.1 INFO:Package:building with make bz2 1.0.6 DEBUG:Package:make PREFIX=/home/nd48/pheniqs-master/bin/trunk_static/install INFO:Package:installing with make bz2 1.0.6 DEBUG:Package:make install PREFIX=/home/nd48/pheniqs-master/bin/trunk_static/install DEBUG:Package:fetching https://tukaani.org/xz/xz-5.2.4.tar.bz2 INFO:Package:downloaded archive saved xz 5.2.4 50ad451279404fb5206e23c7b1ba9c4aa858c994 INFO:Package:unpacking xz 5.2.4 INFO:Package:configuring make environment xz 5.2.4 DEBUG:Package:./configure --prefix=/home/nd48/pheniqs-master/bin/trunk_static/install --enable-static INFO:Package:building with make xz 5.2.4 DEBUG:Package:make INFO:Package:installing with make xz 5.2.4 DEBUG:Package:make install DEBUG:Package:fetching https://github.com/ebiggers/libdeflate/archive/v1.0.tar.gz INFO:Package:downloaded archive saved libdeflate 1.0 17da81b2a058906f087e797fc69399c606a2c011 INFO:Package:unpacking libdeflate 1.0 INFO:Package:building with make libdeflate 1.0 DEBUG:Package:make CC=gcc DEBUG:Package:copying /home/nd48/pheniqs-master/bin/trunk_static/package/libdeflate-1.0/libdeflate.a to /home/nd48/pheniqs-master/bin/trunk_static/install/lib DEBUG:Package:copying /home/nd48/pheniqs-master/bin/trunk_static/package/libdeflate-1.0/libdeflate.h to /home/nd48/pheniqs-master/bin/trunk_static/install/include DEBUG:Package:copying /home/nd48/pheniqs-master/bin/trunk_static/package/libdeflate-1.0/libdeflate.so to /home/nd48/pheniqs-master/bin/trunk_static/install/lib DEBUG:Package:fetching https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 INFO:Package:downloaded archive saved htslib 1.9 21be5187203df30637dda2e1133cae2e833ef050 INFO:Package:unpacking htslib 1.9 INFO:Package:configuring make environment htslib 1.9 DEBUG:Package:./configure --prefix=/home/nd48/pheniqs-master/bin/trunk_static/install --disable-libcurl INFO:Package:building with make htslib 1.9 DEBUG:Package:make INFO:Package:installing with make htslib 1.9 DEBUG:Package:make install DEBUG:Package:fetching https://github.com/miloyip/rapidjson/archive/v1.1.0.tar.gz INFO:Package:downloaded archive saved rapidjson 1.1.0 a3e0d043ad3c2d7638ffefa3beb30a77c71c869f INFO:Package:unpacking rapidjson 1.1.0 DEBUG:Package:copying rapidjson 1.1.0 header files to /home/nd48/pheniqs-master/bin/trunk_static/install/include DEBUG:Package:fetching https://codeload.github.com/biosails/pheniqs/zip/HEAD INFO:Package:downloaded archive saved pheniqs 2.0-trunk None INFO:Package:unpacking pheniqs 2.0-trunk INFO:Package:building with make pheniqs 2.0-trunk DEBUG:Package:make PREFIX=/home/nd48/pheniqs-master/bin/trunk_static/install with-static=1 PHENIQS_ZLIB_VERSION=1.2.11 PHENIQS_BZIP2_VERSION=1.0.6 PHENIQS_XZ_VERSION=5.2.4 PHENIQS_LIBDEFLATE_VERSION=1.0 PHENIQS_HTSLIB_VERSION=1.9 PHENIQS_RAPIDJSON_VERSION=1.1.0 2 version.h generated with PHENIQS_VERSION 2.0.3 configuration.h command line interface configuration generated. zsh completion _pheniqs generated. g++ -Wall -Wsign-compare -I/home/nd48/pheniqs-master/bin/trunk_static/install/include -std=c++11 -O3 -c -o json.o json.cpp

cc1plus: error: unrecognized command line option "-std=c++11" make: *** [json.o] Error 1

CRITICAL:main:make returned 2`

Below is the error log, more bin/trunk_static/error configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support

moonwatcher commented 6 years ago

interesting... htslib can build with libcurl but the current setup does not. I can either explicitly ask to build it without or add libcurl to the build. interesting that it only fails on Centos. Where can I run tests on such a Centos server?

moonwatcher commented 6 years ago

oh wait, the error log thing about libcurl is just a warning. it failed because the compiler does not recognize "-std=c++11". Pheniqs is written in C++11, it wont compile on old compilers that dont support it, which compiler is this environment setup with?

jerowe commented 6 years ago

@nizardrou , were you on dalma? Did you run module load gcc?

twaddlac commented 6 years ago

Not sure what all has been done regarding deploying this, but is this dockerized yet? Shouldn't that take care of most if not all of these issues?

moonwatcher commented 6 years ago

As far as I know gcc only fully supports C++11 since 4.8.1

I don’t really see the point of spending time discussing building on compilers prior to that.