Closed nickschurch closed 6 years ago
jts
commented
6 years ago Hi Nick,
Nanopolish compiled without problems (those warnings can be ignored) but it couldn't find the core C++ libraries at runtime. It looks like you installed GCC using conda, maybe there is a problem with your build or environment?
Jared
nickschurch
commented
6 years ago I've tried several GCC installs with anaconda and they all list the same error. Does it repeat for you? What would you suggest - installing GCC manually in the conda env?
jts
commented
6 years ago can you try conda install libgcc?
nickschurch
commented
6 years ago no joy I'm afraid, same errors....
> conda install --name nanopolish libgcc
Fetching package metadata .........
Solving package specifications: .
Package plan for installation in environment /cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish:
The following NEW packages will be INSTALLED:
libgcc: 5.2.0-0
Proceed ([y]/n)? y
libgcc-5.2.0-0 100% |##############################################################################################################################################################################################| Time: 0:00:00 8.84 MB/s
> source activate nanopolish
(nanopolish) bash-4.1$ cd nanopolish/
(nanopolish) bash-4.1$ ./nanopolish
./nanopolish: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by ./nanopolish)
./nanopolish: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.7' not found (required by ./nanopolish)Can you recompile nanopolish after installing that package? Also please make sure to use gcc-5.2.0-0
nickschurch
commented
6 years ago Still no joy - and there was me thinking that controlled environment management like conda would simplify things! lesigh Struggling to find a conda gcc 5.2.0-0 install. Closes I have found so far is 5-5.2.0-1. With that (after make clean):
bash-4.1$ conda install -c psi4 gcc-5 --name nanopolish
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish:
The following NEW packages will be INSTALLED:
gcc-5: 5.2.0-1 psi4
Proceed ([y]/n)? y
gcc-5-5.2.0-1. 100% |##############################################################################################################################################################################################| Time: 0:00:04 17.27 MB/s
bash-4.1$ source activate nanopolish
(nanopolish) bash-4.1$ which gcc
/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/bin/gcc
(nanopolish) bash-4.1$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/libexec/gcc/x86_64-unknown-linux-gnu/5.2.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --prefix=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc --with-gxx-include-dir=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/include/c++ --bindir=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/bin --datarootdir=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/share --libdir=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/lib --with-gmp=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish --with-mpfr=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish --with-mpc=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish --with-isl=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish --with-cloog=/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish --enable-checking=release --with-tune=generic --disable-multilib
Thread model: posix
gcc version 5.2.0 (GCC)
(nanopolish) bash-4.1$ cd nanopolish/
(nanopolish) bash-4.1$ make
g++ -o src/main/nanopolish.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/main/nanopolish.cpp
g++ -o src/nanopolish_call_methylation.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_call_methylation.cpp
g++ -o src/nanopolish_call_variants.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_call_variants.cpp
g++ -o src/nanopolish_extract.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_extract.cpp
g++ -o src/nanopolish_getmodel.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_getmodel.cpp
g++ -o src/nanopolish_haplotype.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_haplotype.cpp
g++ -o src/nanopolish_index.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_index.cpp
g++ -o src/nanopolish_methyltrain.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_methyltrain.cpp
In file included from ./eigen/Eigen/Core:276:0,
from ./eigen/Eigen/Dense:1,
from src/nanopolish_methyltrain.cpp:45:
./eigen/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder2nd<T> >
^
In file included from /cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/include/c++/bits/stl_function.h:1128:0,
from /cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/include/c++/string:48,
from src/nanopolish_methyltrain.cpp:11:
/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/include/c++/backward/binders.h:143:11: note: declared here
class binder2nd
^
In file included from ./eigen/Eigen/Core:276:0,
from ./eigen/Eigen/Dense:1,
from src/nanopolish_methyltrain.cpp:45:
./eigen/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder1st<T> >
^
In file included from /cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/include/c++/bits/stl_function.h:1128:0,
from /cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/include/c++/string:48,
from src/nanopolish_methyltrain.cpp:11:
/cluster/gjb_lab/nschurch/cluster_installs/miniconda2/envs/nanopolish/gcc/include/c++/backward/binders.h:108:11: note: declared here
class binder1st
^
g++ -o src/nanopolish_phase_reads.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_phase_reads.cpp
src/nanopolish_phase_reads.cpp: In function ‘int phase_reads_main(int, char**)’:
src/nanopolish_phase_reads.cpp:378:55: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(sam_out, processor.get_bam_header());
^
g++ -o src/nanopolish_raw_loader.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_raw_loader.cpp
g++ -o src/nanopolish_read_db.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_read_db.cpp
g++ -o src/nanopolish_scorereads.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_scorereads.cpp
g++ -o src/nanopolish_squiggle_read.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_squiggle_read.cpp
g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp
g++ -o src/nanopolish_variant_db.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/nanopolish_variant_db.cpp
g++ -o src/training_core.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/training_core.cpp
g++ -o src/hmm/nanopolish_duration_model.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/hmm/nanopolish_duration_model.cpp
g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp
g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/hmm/nanopolish_transition_parameters.cpp
g++ -o src/common/fs_support.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/fs_support.cpp
g++ -o src/common/logsum.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/logsum.cpp
g++ -o src/common/nanopolish_alphabet.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/nanopolish_alphabet.cpp
g++ -o src/common/nanopolish_bam_processor.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/nanopolish_bam_processor.cpp
g++ -o src/common/nanopolish_bam_utils.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/nanopolish_bam_utils.cpp
g++ -o src/common/nanopolish_common.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/nanopolish_common.cpp
g++ -o src/common/nanopolish_iupac.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/nanopolish_iupac.cpp
g++ -o src/common/nanopolish_klcs.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/nanopolish_klcs.cpp
g++ -o src/common/nanopolish_variant.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/common/nanopolish_variant.cpp
g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/alignment/nanopolish_alignment_db.cpp
g++ -o src/alignment/nanopolish_anchor.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/alignment/nanopolish_anchor.cpp
g++ -o src/alignment/nanopolish_eventalign.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/alignment/nanopolish_eventalign.cpp
src/alignment/nanopolish_eventalign.cpp: In function ‘void emit_sam_header(samFile*, const bam_hdr_t*)’:
src/alignment/nanopolish_eventalign.cpp:236:27: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
src/alignment/nanopolish_eventalign.cpp: In function ‘void emit_event_alignment_sam(htsFile*, const SquiggleRead&, const bam_hdr_t*, const bam1_t*, const std::vector<EventAlignment>&)’:
src/alignment/nanopolish_eventalign.cpp:375:43: warning: ignoring return value of ‘int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_write1(fp, base_hdr, event_record);
^
g++ -o src/pore_model/nanopolish_model_names.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/pore_model/nanopolish_model_names.cpp
g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/pore_model/nanopolish_poremodel.cpp
g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/pore_model/nanopolish_pore_model_set.cpp
cc -o src/thirdparty/stdaln.o -c -O3 -std=c99 -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -I./include -fPIC src/thirdparty/stdaln.c
cc -o src/thirdparty/scrappie/event_detection.o -c -O3 -std=c99 -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -I./include -fPIC src/thirdparty/scrappie/event_detection.c
cc -o src/thirdparty/scrappie/scrappie_common.o -c -O3 -std=c99 -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -I./include -fPIC src/thirdparty/scrappie/scrappie_common.c
cc -o src/thirdparty/scrappie/util.o -c -O3 -std=c99 -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -I./include -fPIC src/thirdparty/scrappie/util.c
g++ -o nanopolish -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/main/nanopolish.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/training_core.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_poremodel.o src/pore_model/nanopolish_pore_model_set.o src/thirdparty/stdaln.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/scrappie/util.o ./htslib/libhts.a ./lib/libhdf5.a -lz -lrt -ldl
g++ -o src/test/nanopolish_test.o -c -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/test/nanopolish_test.cpp
g++ -o nanopolish_test -g -O3 -std=c++11 -fopenmp -fsigned-char -I./include -I./htslib -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./eigen/ -fPIC src/test/nanopolish_test.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/training_core.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_poremodel.o src/pore_model/nanopolish_pore_model_set.o src/thirdparty/stdaln.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/scrappie/util.o ./htslib/libhts.a ./lib/libhdf5.a -lz -lrt -ldl
(nanopolish) bash-4.1$ ./nanopolish
./nanopolish: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.7' not found (required by ./nanopolish)
./nanopolish: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./nanopolish)
./nanopolish: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by ./nanopolish)
./nanopolish: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./nanopolish)Nick Loman updated the nanopolish conda package to 0.8.5 last week (this is the latest release). Maybe use that?
jts
commented
6 years ago Hi @nickschurch,
Is this still an issue?
Jared
nickschurch
commented
6 years ago I'm still having a problem with this when installing from the github repo. Installing in a clean conda env from the bioconda nanopolish (0.9.0) seems to install correctly, but when I try and run nanopolish I get a different error:
nanopolish: error while loading shared libraries: libhdf5.so.10: cannot open shared object file: No such file or directory```
This is a pretty odd error since the hdf5 v1.10.2-hba1933b_1 is being installed by the package...@nickloman any ideas?
druvus
commented
6 years ago @nickschurch I just checked that the installation worked in a clean conda environment so I think you are picking up hdf5 from default channel instead of conda-forge. Could you please check that you have conda channels set up correctly. See information here.
nickschurch
commented
6 years ago Ack! Your absolutely right - I hadn't added the conda-forge to the new conda env. All working with nanopolish 0.9 now.
jts
commented
6 years ago Great! Thanks for the help @druvus
TumuhimbisePeninah
commented
4 years ago @druvus i have been trying to install nanopolish and using some of the solutions provided here for Nick because i have a similar problem. the make command keeps failing.
i used this code provided on the repo
git clone --recursive https://github.com/jts/nanopolish.git cd nanopolish git checkout v0.9.2 make
this is what i keep getting
SUMMARY OF THE HDF5 CONFIGURATION
================================= HDF5 Version: 1.8.14
Configured on: Thu Aug 20 10:11:30 UTC 2020
Configured by: root@c8755fcc9ba8
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux c8755fcc9ba8 4.15.0-101-generic #102-Ubuntu SMP Mon May 11 10:07:26 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries: static, shared
Installation point: /opt/nanopolish/hdf5-1.8.14/.. Compilation Mode: production
C Compiler: /usr/bin/gcc
CFLAGS:
H5_CFLAGS: -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yesStatically Linked Executables: no LDFLAGS: H5_LDFLAGS: AM_LDFLAGS: -L/opt/nanopolish/hdf5-1.8.14/../lib Extra libraries: -lpthread -ldl -lm Archiver: ar Ranlib: ranlib Debugged Packages: API Tracing: no
Fortran: no
C++: no Parallel HDF5: no
High Level library: yes
Threadsafety: yes
Default API Mapping: v18With Deprecated Public Symbols: yes I/O filters (external): I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset MPE: no Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no Strict File Format Checks: no Optimization Instrumentation: no Large File Support (LFS): yes make[1]: Entering directory '/opt/nanopolish/hdf5-1.8.14' Making all in src make[2]: Entering directory '/opt/nanopolish/hdf5-1.8.14/src' make all-am make[3]: Entering directory '/opt/nanopolish/hdf5-1.8.14/src' CC H5.lo In file included from H5public.h:37:0, from H5private.h:29, from H5.c:24: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
^~~
In file included from H5.c:27:0:
H5Eprivate.h:35:32: warning: anonymous variadic macros were introduced in C99 [-Wvariadic-macros]
^~~In file included from H5.c:27:0: H5Eprivate.h:41:33: warning: anonymous variadic macros were introduced in C99 [-Wvariadic-macros]
^~~H5Eprivate.h:55:40: warning: anonymous variadic macros were introduced in C99 [-Wvariadic-macros]
^~~H5Eprivate.h:67:40: warning: anonymous variadic macros were introduced in C99 [-Wvariadic-macros]
^~~In file included from H5.c:24:0: H5.c: In function 'H5_init_library': H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:181:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize error interface")
^~~
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:183:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize property list interface")
^~~
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:185:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize datatype interface")
^~~
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:187:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize dataset interface")
^~~
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:189:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize metadata caching interface")
^~~
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:191:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, FAIL, "unable to initialize link interface")
^~~
H5.c: In function 'H5garbage_collect':
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5private.h:1861:11: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, err, \
^~~
H5private.h:1876:5: note: in expansion of macro 'FUNC_ENTER_API_INIT'
FUNC_ENTER_API_INIT(err); \
^~~~~~~
H5.c:415:5: note: in expansion of macro 'FUNC_ENTER_API'
FUNC_ENTER_API(FAIL)
^~~~~~
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:420:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTGC, FAIL, "can't garbage collect objects")
^~~
H5.c: In function 'H5set_free_list_limits':
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5private.h:1861:11: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, err, \
^~~
H5private.h:1876:5: note: in expansion of macro 'FUNC_ENTER_API_INIT'
FUNC_ENTER_API_INIT(err); \
^~~~~~~
H5.c:467:5: note: in expansion of macro 'FUNC_ENTER_API'
FUNC_ENTER_API(FAIL)
^~~~~~
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5.c:474:9: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTSET, FAIL, "can't set garbage collection limits")
^~~
H5.c: In function 'H5get_libversion':
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5private.h:1861:11: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, err, \
^~~
H5private.h:1876:5: note: in expansion of macro 'FUNC_ENTER_API_INIT'
FUNC_ENTER_API_INIT(err); \
^~~~~~~
H5.c:610:5: note: in expansion of macro 'FUNC_ENTER_API'
FUNC_ENTER_API(FAIL)
^~~~~~
H5.c: In function 'H5check_version':
H5.c:662:5: warning: string length '526' is greater than the length '509' ISO C90 compilers are required to support [-Woverlength-strings]
static const char *version_mismatch_warning = VERSION_MISMATCH_WARNING;
^~
In file included from H5.c:24:0:
H5.c: In function 'H5open':
H5private.h:1539:14: warning: ISO C90 does not support 'func' predefined identifier [-Wpedantic]
^H5Eprivate.h:35:70: note: in expansion of macro 'FUNC'
^~~~H5Eprivate.h:42:4: note: in expansion of macro 'HERROR'
HERROR(maj, min, VA_ARGS); \
^~
H5Eprivate.h:68:4: note: in expansion of macro 'HCOMMON_ERROR'
HCOMMON_ERROR(maj, min, VA_ARGS); \
^~~~~
H5private.h:1861:11: note: in expansion of macro 'HGOTO_ERROR'
HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, err, \
^~~
H5private.h:1887:5: note: in expansion of macro 'FUNC_ENTER_API_INIT'
FUNC_ENTER_API_INIT(err); \
^~~~~~~
H5.c:779:5: note: in expansion of macro 'FUNC_ENTER_API_NOCLEAR'
FUNC_ENTER_API_NOCLEAR(FAIL)
^~~~~~
CC H5checksum.lo
In file included from H5public.h:37:0,
from H5private.h:29,
from H5checksum.c:35:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
^~~
H5checksum.c: In function 'H5_checksum_lookup3':
H5checksum.c:411:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 12: c+=((uint32_t)k[11])<<24;
~^~~~~~~
H5checksum.c:412:9: note: here
case 11: c+=((uint32_t)k[10])<<16;
^~~~
H5checksum.c:412:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 11: c+=((uint32_t)k[10])<<16;
~^~~~~~~
H5checksum.c:413:9: note: here
case 10: c+=((uint32_t)k[9])<<8;
^~~~
H5checksum.c:413:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 10: c+=((uint32_t)k[9])<<8;
~^~~~~
H5checksum.c:414:9: note: here
case 9 : c+=k[8];
^~~~
H5checksum.c:414:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 9 : c+=k[8];
~^~
H5checksum.c:415:9: note: here
case 8 : b+=((uint32_t)k[7])<<24;
^~~~
H5checksum.c:415:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 8 : b+=((uint32_t)k[7])<<24;
~^~~~~~
H5checksum.c:416:9: note: here
case 7 : b+=((uint32_t)k[6])<<16;
^~~~
H5checksum.c:416:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 7 : b+=((uint32_t)k[6])<<16;
~^~~~~~
H5checksum.c:417:9: note: here
case 6 : b+=((uint32_t)k[5])<<8;
^~~~
H5checksum.c:417:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 6 : b+=((uint32_t)k[5])<<8;
~^~~~~
H5checksum.c:418:9: note: here
case 5 : b+=k[4];
^~~~
H5checksum.c:418:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 5 : b+=k[4];
~^~
H5checksum.c:419:9: note: here
case 4 : a+=((uint32_t)k[3])<<24;
^~~~
H5checksum.c:419:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 4 : a+=((uint32_t)k[3])<<24;
~^~~~~~
H5checksum.c:420:9: note: here
case 3 : a+=((uint32_t)k[2])<<16;
^~~~
H5checksum.c:420:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 3 : a+=((uint32_t)k[2])<<16;
~^~~~~~
H5checksum.c:421:9: note: here
case 2 : a+=((uint32_t)k[1])<<8;
^~~~
H5checksum.c:421:19: warning: this statement may fall through [-Wimplicit-fallthrough=]
case 2 : a+=((uint32_t)k[1])<<8;
~^~~~~
H5checksum.c:422:9: note: here
case 1 : a+=k[0];
^~~~
najohink
commented
2 years ago @TumuhimbisePeninah Did you ever figure out a solution to this problem? I too am encountering the same issue.
best, S
nicolo-tellini
commented
2 years ago Hello,
any solutions to that error ?
best,
Nic
TumuhimbisePeninah
commented
2 years ago No i did not, and failed to find an alternative
On Fri, 26 Aug 2022 at 14:25, nt @.***> wrote:
Hello,
any solutions to that error ?
best,
Nic
— Reply to this email directly, view it on GitHub https://github.com/jts/nanopolish/issues/298#issuecomment-1228375919, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOAMGSG7ZS46QBJIERLVQGDV3CSRJANCNFSM4EIIOSGQ . You are receiving this because you were mentioned.Message ID: @.***>
jts
commented
2 years ago Sorry for missing this. @TumuhimbisePeninah if you still want to try to install nanopolish please feel free to open a new issue and I'll try to help you. @nicolo-tellini I'll help you over in the issue you opened (I'm back from holiday now)
I'm trying to install nanopolish from the github repo into a clean conda Centos 6.8 environment with gcc 4.8.5 but its failing. Here are the commands and output (log of the make command is attached):
makenanopolish.log