Comments (6)
cb4github
commented on August 17, 2024
1
See my mention here for details, but per @andrewdavidsmith's request, I've copied from there my result including the same error as @shaohuaihan.
make[4]: Entering directory `/lustre/project/<PI>/build/centos7/dnmtools/src/abismal'
depbase=`echo src/abismal.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I ./src/smithlab_cpp -I ./src/bamxx -fopenmp -O3 -MT src/abismal.o -MD -MP -MF $depbase.Tpo -c -o src/abismal.o src/abismal.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from src/abismal.cpp:34:
src/AbismalAlign.hpp:215:50: error: unknown vectorizer cost model 'very-cheap'
#pragma GCC optimize("vect-cost-model=very-cheap")
^
src/AbismalAlign.hpp:215:50: note: valid arguments to '-fvect-cost-model=' are: cheap dynamic unlimited; did you mean 'cheap'?
I hope this helps.
Best,
CB
from dnmtools.
andrewdavidsmith
commented on August 17, 2024
Please give full information or I can't help.
from dnmtools.
andrewdavidsmith
commented on August 17, 2024
@cb4github Thanks for the details on this. I think it should be fixed as of commit #217 . Let me know if you are able to test it. You might also directly try the same thing in the abismal repo. That's where I made the change initially and then updated them in dnmtools.
from dnmtools.
cb4github
commented on August 17, 2024
@andrewdavidsmith I tried building the new master - still using gcc/8.5.0 - and still received errors indicating c++17 is insufficient such as the following.
../../../src/abismal/src/AbismalIndex.cpp:41:12: error: 'std::inclusive_scan' has not been declared
using std::inclusive_scan;
^~~~~~~~~~~~~~
module load gcc/8.5.0 htslib/1.19 autoconf/2.71 htslib/1.20 gsl/2.6
Here's the resulting (warning: entire) log of my attempted make. Thanks again.
Command follows...
make
Output follows...
make all-recursive
make[1]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build'
Making all in src/smithlab_cpp
make[2]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
make all-am
make[3]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT GenomicRegion.o -MD -MP -MF .deps/GenomicRegion.Tpo -c -o GenomicRegion.o ../../../src/smithlab_cpp/GenomicRegion.cpp
In file included from ../../../src/smithlab_cpp/GenomicRegion.hpp:27,
from ../../../src/smithlab_cpp/GenomicRegion.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/GenomicRegion.Tpo .deps/GenomicRegion.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT MappedRead.o -MD -MP -MF .deps/MappedRead.Tpo -c -o MappedRead.o ../../../src/smithlab_cpp/MappedRead.cpp
In file included from ../../../src/smithlab_cpp/GenomicRegion.hpp:27,
from ../../../src/smithlab_cpp/MappedRead.hpp:26,
from ../../../src/smithlab_cpp/MappedRead.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/MappedRead.Tpo .deps/MappedRead.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT OptionParser.o -MD -MP -MF .deps/OptionParser.Tpo -c -o OptionParser.o ../../../src/smithlab_cpp/OptionParser.cpp
In file included from ../../../src/smithlab_cpp/OptionParser.cpp:37:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/OptionParser.Tpo .deps/OptionParser.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT QualityScore.o -MD -MP -MF .deps/QualityScore.Tpo -c -o QualityScore.o ../../../src/smithlab_cpp/QualityScore.cpp
In file included from ../../../src/smithlab_cpp/QualityScore.cpp:26:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/QualityScore.Tpo .deps/QualityScore.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT chromosome_utils.o -MD -MP -MF .deps/chromosome_utils.Tpo -c -o chromosome_utils.o ../../../src/smithlab_cpp/chromosome_utils.cpp
In file included from ../../../src/smithlab_cpp/GenomicRegion.hpp:27,
from ../../../src/smithlab_cpp/chromosome_utils.hpp:37,
from ../../../src/smithlab_cpp/chromosome_utils.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/chromosome_utils.Tpo .deps/chromosome_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT bisulfite_utils.o -MD -MP -MF .deps/bisulfite_utils.Tpo -c -o bisulfite_utils.o ../../../src/smithlab_cpp/bisulfite_utils.cpp
mv -f .deps/bisulfite_utils.Tpo .deps/bisulfite_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT smithlab_os.o -MD -MP -MF .deps/smithlab_os.Tpo -c -o smithlab_os.o ../../../src/smithlab_cpp/smithlab_os.cpp
In file included from ../../../src/smithlab_cpp/smithlab_os.cpp:30:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/smithlab_os.Tpo .deps/smithlab_os.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT smithlab_utils.o -MD -MP -MF .deps/smithlab_utils.Tpo -c -o smithlab_utils.o ../../../src/smithlab_cpp/smithlab_utils.cpp
In file included from ../../../src/smithlab_cpp/smithlab_utils.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/smithlab_utils.Tpo .deps/smithlab_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT zlib_wrapper.o -MD -MP -MF .deps/zlib_wrapper.Tpo -c -o zlib_wrapper.o ../../../src/smithlab_cpp/zlib_wrapper.cpp
mv -f .deps/zlib_wrapper.Tpo .deps/zlib_wrapper.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT dna_four_bit.o -MD -MP -MF .deps/dna_four_bit.Tpo -c -o dna_four_bit.o ../../../src/smithlab_cpp/dna_four_bit.cpp
mv -f .deps/dna_four_bit.Tpo .deps/dna_four_bit.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT cigar_utils.o -MD -MP -MF .deps/cigar_utils.Tpo -c -o cigar_utils.o ../../../src/smithlab_cpp/cigar_utils.cpp
mv -f .deps/cigar_utils.Tpo .deps/cigar_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT sam_record.o -MD -MP -MF .deps/sam_record.Tpo -c -o sam_record.o ../../../src/smithlab_cpp/sam_record.cpp
In file included from ../../../src/smithlab_cpp/sam_record.cpp:26:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
mv -f .deps/sam_record.Tpo .deps/sam_record.Po
rm -f libsmithlab_cpp.a
ar cru libsmithlab_cpp.a GenomicRegion.o MappedRead.o OptionParser.o QualityScore.o chromosome_utils.o bisulfite_utils.o smithlab_os.o smithlab_utils.o zlib_wrapper.o dna_four_bit.o cigar_utils.o sam_record.o
ranlib libsmithlab_cpp.a
make[3]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
make[2]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
Making all in src/abismal
make[2]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make all-recursive
make[3]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
Making all in src/smithlab_cpp
make[4]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
make all-am
make[5]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT GenomicRegion.o -MD -MP -MF .deps/GenomicRegion.Tpo -c -o GenomicRegion.o ../../../../../src/abismal/src/smithlab_cpp/GenomicRegion.cpp
mv -f .deps/GenomicRegion.Tpo .deps/GenomicRegion.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT MappedRead.o -MD -MP -MF .deps/MappedRead.Tpo -c -o MappedRead.o ../../../../../src/abismal/src/smithlab_cpp/MappedRead.cpp
mv -f .deps/MappedRead.Tpo .deps/MappedRead.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT OptionParser.o -MD -MP -MF .deps/OptionParser.Tpo -c -o OptionParser.o ../../../../../src/abismal/src/smithlab_cpp/OptionParser.cpp
mv -f .deps/OptionParser.Tpo .deps/OptionParser.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT QualityScore.o -MD -MP -MF .deps/QualityScore.Tpo -c -o QualityScore.o ../../../../../src/abismal/src/smithlab_cpp/QualityScore.cpp
mv -f .deps/QualityScore.Tpo .deps/QualityScore.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT chromosome_utils.o -MD -MP -MF .deps/chromosome_utils.Tpo -c -o chromosome_utils.o ../../../../../src/abismal/src/smithlab_cpp/chromosome_utils.cpp
mv -f .deps/chromosome_utils.Tpo .deps/chromosome_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT bisulfite_utils.o -MD -MP -MF .deps/bisulfite_utils.Tpo -c -o bisulfite_utils.o ../../../../../src/abismal/src/smithlab_cpp/bisulfite_utils.cpp
mv -f .deps/bisulfite_utils.Tpo .deps/bisulfite_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT smithlab_os.o -MD -MP -MF .deps/smithlab_os.Tpo -c -o smithlab_os.o ../../../../../src/abismal/src/smithlab_cpp/smithlab_os.cpp
mv -f .deps/smithlab_os.Tpo .deps/smithlab_os.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT smithlab_utils.o -MD -MP -MF .deps/smithlab_utils.Tpo -c -o smithlab_utils.o ../../../../../src/abismal/src/smithlab_cpp/smithlab_utils.cpp
mv -f .deps/smithlab_utils.Tpo .deps/smithlab_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT zlib_wrapper.o -MD -MP -MF .deps/zlib_wrapper.Tpo -c -o zlib_wrapper.o ../../../../../src/abismal/src/smithlab_cpp/zlib_wrapper.cpp
mv -f .deps/zlib_wrapper.Tpo .deps/zlib_wrapper.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT dna_four_bit.o -MD -MP -MF .deps/dna_four_bit.Tpo -c -o dna_four_bit.o ../../../../../src/abismal/src/smithlab_cpp/dna_four_bit.cpp
mv -f .deps/dna_four_bit.Tpo .deps/dna_four_bit.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT cigar_utils.o -MD -MP -MF .deps/cigar_utils.Tpo -c -o cigar_utils.o ../../../../../src/abismal/src/smithlab_cpp/cigar_utils.cpp
mv -f .deps/cigar_utils.Tpo .deps/cigar_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp -I/lustre/project/PI/apps/htslib/1.20/include -Wall -O3 -MT sam_record.o -MD -MP -MF .deps/sam_record.Tpo -c -o sam_record.o ../../../../../src/abismal/src/smithlab_cpp/sam_record.cpp
mv -f .deps/sam_record.Tpo .deps/sam_record.Po
rm -f libsmithlab_cpp.a
ar cru libsmithlab_cpp.a GenomicRegion.o MappedRead.o OptionParser.o QualityScore.o chromosome_utils.o bisulfite_utils.o smithlab_os.o smithlab_utils.o zlib_wrapper.o dna_four_bit.o cigar_utils.o sam_record.o
ranlib libsmithlab_cpp.a
make[5]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
make[4]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
make[4]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
depbase=`echo src/abismal.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/abismal -I ../../../src/abismal/src/smithlab_cpp -I ../../../src/abismal/src/bamxx -I/lustre/project/PI/apps/htslib/1.20/include -fopenmp -Wall -Wextra -Wpedantic -Wno-unknown-attributes -O3 -DNDEBUG -MT src/abismal.o -MD -MP -MF $depbase.Tpo -c -o src/abismal.o ../../../src/abismal/src/abismal.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from ../../../src/abismal/src/abismal.cpp:34:
../../../src/abismal/src/AbismalAlign.hpp:100:2: warning: extra ';' [-Wpedantic]
}; // namespace simple_aln
^
In file included from ../../../src/abismal/src/AbismalIndex.hpp:33,
from ../../../src/abismal/src/abismal.cpp:35:
../../../src/abismal/src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
In file included from ../../../src/abismal/src/abismal.cpp:35:
../../../src/abismal/src/AbismalIndex.hpp:93:2: warning: extra ';' [-Wpedantic]
};
^
In file included from ../../../src/abismal/src/abismal.cpp:37:
../../../src/abismal/src/bamxx/bamxx.hpp:194:2: warning: extra ';' [-Wpedantic]
}; // namespace bamxx
^
cc1plus: warning: unrecognized command line option '-Wno-unknown-attributes'
depbase=`echo src/abismalidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/abismal -I ../../../src/abismal/src/smithlab_cpp -I ../../../src/abismal/src/bamxx -I/lustre/project/PI/apps/htslib/1.20/include -fopenmp -Wall -Wextra -Wpedantic -Wno-unknown-attributes -O3 -DNDEBUG -MT src/abismalidx.o -MD -MP -MF $depbase.Tpo -c -o src/abismalidx.o ../../../src/abismal/src/abismalidx.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from ../../../src/abismal/src/abismalidx.cpp:19:
../../../src/abismal/src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
In file included from ../../../src/abismal/src/abismalidx.cpp:24:
../../../src/abismal/src/AbismalIndex.hpp:93:2: warning: extra ';' [-Wpedantic]
};
^
cc1plus: warning: unrecognized command line option '-Wno-unknown-attributes'
depbase=`echo src/AbismalIndex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/abismal -I ../../../src/abismal/src/smithlab_cpp -I ../../../src/abismal/src/bamxx -I/lustre/project/PI/apps/htslib/1.20/include -fopenmp -Wall -Wextra -Wpedantic -Wno-unknown-attributes -O3 -DNDEBUG -MT src/AbismalIndex.o -MD -MP -MF $depbase.Tpo -c -o src/AbismalIndex.o ../../../src/abismal/src/AbismalIndex.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from ../../../src/abismal/src/AbismalIndex.hpp:33,
from ../../../src/abismal/src/AbismalIndex.cpp:18:
../../../src/abismal/src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
};
^
In file included from ../../../src/abismal/src/AbismalIndex.cpp:18:
../../../src/abismal/src/AbismalIndex.hpp:93:2: warning: extra ';' [-Wpedantic]
};
^
In file included from ../../../src/abismal/src/AbismalIndex.cpp:32:
../../../src/abismal/src/bamxx/bamxx.hpp:194:2: warning: extra ';' [-Wpedantic]
}; // namespace bamxx
^
../../../src/abismal/src/AbismalIndex.cpp:41:12: error: 'std::inclusive_scan' has not been declared
using std::inclusive_scan;
^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp: In member function 'void AbismalIndex::select_two_letter_positions()':
../../../src/abismal/src/AbismalIndex.cpp:460:20: error: found ':' in nested-name-specifier, expected '::'
for (auto &block : blocks) {
^
::
../../../src/abismal/src/AbismalIndex.cpp:460:14: error: 'block' has not been declared
for (auto &block : blocks) {
^~~~~
../../../src/abismal/src/AbismalIndex.cpp:460:28: error: qualified-id in declaration before ')' token
for (auto &block : blocks) {
^
../../../src/abismal/src/AbismalIndex.cpp:493:4: error: expected ';' before 'if'
}
^
;
if (VERBOSE) clog << delta_seconds(s_time) << endl;
~~
../../../src/abismal/src/AbismalIndex.cpp:494:3: error: expected primary-expression before 'if'
if (VERBOSE) clog << delta_seconds(s_time) << endl;
^~
../../../src/abismal/src/AbismalIndex.cpp:495:1: error: expected primary-expression before '}' token
}
^
../../../src/abismal/src/AbismalIndex.cpp:494:54: error: expected ')' before '}' token
if (VERBOSE) clog << delta_seconds(s_time) << endl;
^
)
}
~
../../../src/abismal/src/AbismalIndex.cpp:460:7: note: to match this '('
for (auto &block : blocks) {
^
../../../src/abismal/src/AbismalIndex.cpp:495:1: error: expected primary-expression before '}' token
}
^
../../../src/abismal/src/AbismalIndex.cpp:460:3: error: expected iteration declaration or initialization
for (auto &block : blocks) {
^~~
../../../src/abismal/src/AbismalIndex.cpp: In member function 'void AbismalIndex::hash_genome()':
../../../src/abismal/src/AbismalIndex.cpp:505:3: error: 'inclusive_scan' was not declared in this scope
inclusive_scan(begin(counter), end(counter), begin(counter));
^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp:507:3: error: 'inclusive_scan' was not declared in this scope
inclusive_scan(begin(counter_t), end(counter_t), begin(counter_t));
^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp:509:3: error: 'inclusive_scan' was not declared in this scope
inclusive_scan(begin(counter_a), end(counter_a), begin(counter_a));
^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp: In member function 'void AbismalIndex::compress_dp()':
../../../src/abismal/src/AbismalIndex.cpp:665:20: error: found ':' in nested-name-specifier, expected '::'
for (auto &block : blocks) {
^
::
../../../src/abismal/src/AbismalIndex.cpp:665:14: error: 'block' has not been declared
for (auto &block : blocks) {
^~~~~
../../../src/abismal/src/AbismalIndex.cpp:665:28: error: qualified-id in declaration before ')' token
for (auto &block : blocks) {
^
../../../src/abismal/src/AbismalIndex.cpp:757:4: error: expected ';' before 'max_candidates'
}
^
;
../../../src/abismal/src/AbismalIndex.cpp:759:3:
max_candidates = 100u; // GS: this is a heuristic
~~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp:760:3: error: expected primary-expression before 'if'
if (VERBOSE) clog << delta_seconds(s_time) << endl;
^~
../../../src/abismal/src/AbismalIndex.cpp:759:25: error: expected ')' before 'if'
max_candidates = 100u; // GS: this is a heuristic
^
)
if (VERBOSE) clog << delta_seconds(s_time) << endl;
~~
../../../src/abismal/src/AbismalIndex.cpp:665:7: note: to match this '('
for (auto &block : blocks) {
^
../../../src/abismal/src/AbismalIndex.cpp:665:3: error: expected iteration declaration or initialization
for (auto &block : blocks) {
^~~
At global scope:
cc1plus: warning: unrecognized command line option '-Wno-unknown-attributes'
make[4]: *** [src/AbismalIndex.o] Error 1
make[4]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build'
make: *** [all] Error 2
from dnmtools.
andrewdavidsmith
commented on August 17, 2024
@cb4github Thanks. I can check it out some more. There are some potential problems that might not be addressable, but we can figure out if these are relevant. It's possible gcc 8.5 doesn't fully support c++17. They always have a list of which parts of the standard they support in each version, and it's rarely 100% until much later. There's also a chance that the "module" is an issue. I don't trust those myself; they are almost as bad as conda for pollution. And what's most likely, but we can fix, is that somewhere I forgot I had to just use c++17, since I've been using c++20 for some time now. If that were the case, my compiler, and the one on github runners, should have complained. Thinking out loud here, but I could use github runners to determine which compilers and versions are supported. Anyway, thanks again and I'll check it out asap.
from dnmtools.
andrewdavidsmith
commented on August 17, 2024
Locking this issues and asking to open a new issue for different problems.
from dnmtools.
Related Issues (20)
- dnmtools diff Error HOT 4
- Calling HMRs on the DNA Methylation Atlas Data HOT 4
- roi "cannot sort data unless all data is loaded" HOT 3
- mlml "error: chrom or pos mismatch in both files" HOT 3
- Keep non-CpG sites after sym command
- Broken progress bar
- roi -M return different values for "number of CpGs in the region" for different count files HOT 3
- roi should check for input files before reporting any problems with arguments
- pmd crash if insufficient data unless verbose mode used HOT 1
- -v flag opposite in guessprotocol
- A question for 'dnmtools allelic' HOT 2
- format: max distance when merging mates seems ignored
- merge -t header seems to be not properly formatted HOT 3
- HMR crash when nothing identified
- bad count line HOT 1
- resolved.
- summary hmr_count is non-zero but hmr output file is empty HOT 5
- Building dnmtools using gcc 8.5.0
- Building dnmtools using gcc 8.5.0 HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from dnmtools.