Can't complete Make on Ubuntu 14.04: #2
Comments
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If you run the command 'ld -lz --verbose' does yours system find a working copy of libz? If not try running 'ldconfig' or restarting your machine. In the Karp directories, after you run cmake does the file /build/karp/karp.dir/link.txt contain a link to a libz library? |
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hello, Thanks for the quick reply! The answer to your first question appears to be no, despite what looked like a successful install. When I run 'ld -lz --verbose', here is the output... ==================================================
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From the verbose output it looks like your system is successfully finding libz at /usr/lib/x86_64-linux-gnu/libz.so, so it is a matter of CMAKE not finding it. Try deleting the build folder and restarting the entire install process. If that doesn't work when try running the cmake command as 'cmake -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu/ ..' |
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Keep trying and keep failing. Couldn't get it to work with Ubuntu 14.04, so I installed Ubuntu 16.04 and tried again. No luck, similar errors. Now trying on my late-2015 macbook pro running OSX Yosemite with updated gcc compiler (4.9, via homebrew). I've listed the outputs of my attempt from the beginning below. It seems no matter what I do, I cannot push this rock up the hill. Three OS's, three strikes. Any insight on the outputs below would be very helpful. Thanks. jrussellmac:src jrussell$ git clone https://github.com/mreppell/Karp.git Then, run 'make'.... jrussellmac:build jrussell$ make then a LARGE amount of text and then... ld: symbol(s) not found for architecture x86_64 |
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For what it's worth (anyone who may end up here with similar issues), I solved this by installing Anaconda3-2.5.0 on my NUC running Ubuntu 16.04. I guess it remedied whatever /lib/x86_64-linux-gnu issues I was having...I'm presuming by installing something I was missing, or putting them in an easier place to find/access? Either way, I successfully made it through 'cmake..' and 'make'. Thanks. |
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I'm glad you were able to get the program to install, thanks for reporting back what worked for you! |
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No prob. I'm curious if you have any pre-made indices available? I am
trying to use Karp as a metagenomics taxonomy classifier, and to have it be
as unbiased as possible, I am trying to make the index from a RefSeq size
DB. But, I run out of memory for this task on my NUC (32 GB of RAM). Does
the index-making process have to hold the *entire* DB in memory? Can you do
it in chunks and combine at the end? Or, do you have any pre-made indices
that would work well for unbiased metagenomics classification?
…-------------------------------------------
Joe Russell, Ph.D.
www.waywardscientist.com
On Mon, Feb 27, 2017 at 6:38 PM, mreppell ***@***.***> wrote:
I'm glad you were able to get the program to install, thanks for reporting
back what worked for you!
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Currently there is not a way to use multiple indices with Karp, and as I have not constructed indices for metagenomic databases I am unable to distribute pre-computed databases. Adding a feature to allow multiple indices (so that a big database can be split during index creation) is a good suggestion for a program update |
Hello,
I am trying to install and compile Karp on an Intel NUC running Ubuntu 14.04. I have cmake version 2.8.12.2
I can successfully run 'cmake ..', but when I run 'make', I get the error pasted below, and no executable in /src. It appears to refer to my zlib installation. I installed zlib using apt-get (sudo apt-get install zlib1g-dev).
I've seen other posts online referring to this error requiring a -lz flag at the end of the make file, (e.g., najoshi/sabre#1)?
Any help solving this is much appreciated! Thanks!
Make error below...
$ make
[ 93%] Built target karp_core
Linking CXX executable karp
libkarp_core.a(ProcessReads.cpp.o): In function
ks_getuntil2(__kstream_t*, int, __kstring_t*, int*, int) [clone .constprop.456]': ProcessReads.cpp:(.text+0x4e): undefined reference togzread'libkarp_core.a(ProcessReads.cpp.o): In function
kseq_read(kseq_t*)': ProcessReads.cpp:(.text+0x2ff): undefined reference togzread'ProcessReads.cpp:(.text+0x377): undefined reference to
gzread' ProcessReads.cpp:(.text+0x548): undefined reference togzread'ProcessReads.cpp:(.text+0x693): undefined reference to
gzread' libkarp_core.a(ProcessReads.cpp.o): In functionSequenceReader::~SequenceReader()':ProcessReads.cpp:(.text+0x1070): undefined reference to
gzclose' ProcessReads.cpp:(.text+0x1084): undefined reference togzclose'libkarp_core.a(ProcessReads.cpp.o): In function
ReadProcessor::WriteInt(std::vector<std::unordered_map<double, std::vector<unsigned int, std::allocator<unsigned int> >, std::hash<double>, std::equal_to<double>, std::allocator<std::pair<double const, std::vector<unsigned int, std::allocator<unsigned int> > > > >, std::allocator<std::unordered_map<double, std::vector<unsigned int, std::allocator<unsigned int> >, std::hash<double>, std::equal_to<double>, std::allocator<std::pair<double const, std::vector<unsigned int, std::allocator<unsigned int> > > > > > >&, gzFile_s*&, gzFile_s*&, std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, LKFilter&, std::unordered_map<unsigned int, bool, std::hash<unsigned int>, std::equal_to<unsigned int>, std::allocator<std::pair<unsigned int const, bool> > >&, gzFile_s*&, std::unordered_map<int, std::string, std::hash<int>, std::equal_to<int>, std::allocator<std::pair<int const, std::string> > >&, gzFile_s*&)': ProcessReads.cpp:(.text+0x1619): undefined reference togzwrite'ProcessReads.cpp:(.text+0x169e): undefined reference to
gzwrite' ProcessReads.cpp:(.text+0x1bc4): undefined reference togzwrite'ProcessReads.cpp:(.text+0x1c4e): undefined reference to
gzwrite' ProcessReads.cpp:(.text+0x1ccd): undefined reference togzwrite'libkarp_core.a(ProcessReads.cpp.o):ProcessReads.cpp:(.text+0x1d66): more undefined references to
gzwrite' follow libkarp_core.a(ProcessReads.cpp.o): In functionSequenceReader::fetchSequences(char*, int, std::vector<std::pair<char const*, int>, std::allocator<std::pair<char const*, int> > >&, std::vector<std::pair<char const*, int>, std::allocator<std::pair<char const*, int> > >&, std::vector<std::pair<char const*, int>, std::allocator<std::pair<char const*, int> > >&)':ProcessReads.cpp:(.text+0x282a): undefined reference to
gzclose' ProcessReads.cpp:(.text+0x283f): undefined reference togzclose'ProcessReads.cpp:(.text+0x2858): undefined reference to
gzopen' ProcessReads.cpp:(.text+0x2b7e): undefined reference togzopen'libkarp_core.a(ProcessReads.cpp.o): In function
ProcessReads(KmerIndex&, ProgramOptions const&, MinCollector&, fastaIndex&, std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&, LKFilter&, EarlyTaxonomy&, HLK&)': ProcessReads.cpp:(.text+0x38be): undefined reference togzopen'ProcessReads.cpp:(.text+0x3917): undefined reference to
gzwrite' ProcessReads.cpp:(.text+0x39b8): undefined reference togzopen'ProcessReads.cpp:(.text+0x3a17): undefined reference to
gzwrite' ProcessReads.cpp:(.text+0x3a59): undefined reference togzread'ProcessReads.cpp:(.text+0x3a6c): undefined reference to
gzclose' ProcessReads.cpp:(.text+0x3ae4): undefined reference togzwrite'ProcessReads.cpp:(.text+0x3b76): undefined reference to
gzopen' ProcessReads.cpp:(.text+0x3bd7): undefined reference togzwrite'ProcessReads.cpp:(.text+0x3c19): undefined reference to
gzread' ProcessReads.cpp:(.text+0x3c2c): undefined reference togzclose'ProcessReads.cpp:(.text+0x3cea): undefined reference to
gzclose' ProcessReads.cpp:(.text+0x4782): undefined reference togzopen'ProcessReads.cpp:(.text+0x4831): undefined reference to
gzopen' ProcessReads.cpp:(.text+0x48a1): undefined reference togzwrite'ProcessReads.cpp:(.text+0x48e3): undefined reference to
gzread' ProcessReads.cpp:(.text+0x48f5): undefined reference togzclose'ProcessReads.cpp:(.text+0x496b): undefined reference to
gzclose' libkarp_core.a(ProcessReads.cpp.o): In functionReadProcessor::operator()()':ProcessReads.cpp:(.text+0x8712): undefined reference to
gzopen' ProcessReads.cpp:(.text+0x879f): undefined reference togzopen'ProcessReads.cpp:(.text+0x8879): undefined reference to
gzopen' ProcessReads.cpp:(.text+0x88bf): undefined reference togzopen'ProcessReads.cpp:(.text+0x8958): undefined reference to
gzopen' ProcessReads.cpp:(.text+0x8b7a): undefined reference togzwrite'ProcessReads.cpp:(.text+0x8c44): undefined reference to
gzclose' ProcessReads.cpp:(.text+0x8c4e): undefined reference togzclose'ProcessReads.cpp:(.text+0x8c58): undefined reference to
gzclose' ProcessReads.cpp:(.text+0x8c65): undefined reference togzclose'ProcessReads.cpp:(.text+0x8c72): undefined reference to
gzclose' libkarp_core.a(karp_like_multi.cpp.o): In functionGetAbundance(LikelihoodProcessor*, int, std::unordered_map<unsigned int, double, std::hash, std::equal_to, std::allocator<std::pair<unsigned int const, double> > >, double, std::string, double)':karp_like_multi.cpp:(.text+0xe4f): undefined reference to
gzopen' karp_like_multi.cpp:(.text+0xede): undefined reference togzread'karp_like_multi.cpp:(.text+0x2174): undefined reference to
gzclose' libkarp_core.a(karp_like_multi.cpp.o): In functionHLK::GetPriors(std::basic_stringstream<char, std::char_traits, std::allocator >&)':karp_like_multi.cpp:(.text+0x2a57): undefined reference to
gzopen' karp_like_multi.cpp:(.text+0x2aa9): undefined reference togzread'libkarp_core.a(KmerIndex.cpp.o): In function
ks_getuntil2(__kstream_t*, int, __kstring_t*, int*, int) [clone .constprop.363]': KmerIndex.cpp:(.text+0x2be): undefined reference togzread'libkarp_core.a(KmerIndex.cpp.o): In function
KmerIndex::BuildTranscripts(ProgramOptions const&)': KmerIndex.cpp:(.text+0x8017): undefined reference togzopen'KmerIndex.cpp:(.text+0x80d5): undefined reference to
gzread' KmerIndex.cpp:(.text+0x8216): undefined reference togzread'KmerIndex.cpp:(.text+0x8401): undefined reference to
gzread' KmerIndex.cpp:(.text+0x8a7e): undefined reference togzread'KmerIndex.cpp:(.text+0x8aea): undefined reference to `gzclose'
collect2: error: ld returned 1 exit status
make[2]: *** [src/karp] Error 1
make[1]: *** [src/CMakeFiles/karp.dir/all] Error 2
make: *** [all] Error 2
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