problem with sdsorter

[Sherif Elsabbagh]

when i tried to use sdosrter i got this message
dyld: Library not loaded: /opt/local/lib/libopenbabel.5.dylib
Referenced from: /Users/sherifelsabbagh/opt/anaconda3/envs/my-rdkit-env/bin/sdsorter.osx
Reason: image not found

although i installed the latest version of obabel.. can you help me with this?

[David Koes]

Your best bet is to build from source to ensure you have compatible libraries. Although that looks like sdsorter was someone provided as part of a conda package, in which case I suggest contacting the maintainer and seeing if they can fix their dependencies.

[Sherif Elsabbagh]

thanks for your comment.. can you tell me how to build it from source..
i just downloaded sdsorter.osx and run it using ./sdsorter.osx after giving permission to it.
is there any other tool that can give the same result ?

[David Koes]

git clone git://git.code.sf.net/p/sdsorter/code sdsorter-code
cd sdsorter-code
make sdsorter

Fix include/library paths to match your system as needed.

[Sherif Elsabbagh]

i am very sorry..
but i didnt understande where to fix this?

is there anything that can do same function as sdsorter?

[David Koes]

What is the error you are getting?

[Sherif Elsabbagh]

g++ main.cpp CommandLine2/CommandLine.cpp -L/usr/local/lib -O3 -g -o Release/sdsorter -I/usr/local/include/openbabel3 -I/usr/include/openbabel3 -lopenbabel -lboost_system -lboost_regex -lboost_filesystem -lboost_iostreams
ld: warning: dylib (/usr/local/lib/libopenbabel.dylib) was built for newer macOS version (11.0) than being linked (10.16)
ld: warning: dylib (/usr/local/lib/libboost_system.dylib) was built for newer macOS version (11.0) than being linked (10.16)
ld: warning: dylib (/usr/local/lib/libboost_regex.dylib) was built for newer macOS version (11.0) than being linked (10.16)
ld: warning: dylib (/usr/local/lib/libboost_filesystem.dylib) was built for newer macOS version (11.0) than being linked (10.16)
ld: warning: dylib (/usr/local/lib/libboost_iostreams.dylib) was built for newer macOS version (11.0) than being linked (10.16)
Undefined symbols for architecture x86_64:
"boost::scoped_static_mutex_lock::scoped_static_mutex_lock(boost::static_mutex&, bool)", referenced from:
boost::object_cache<boost::re_detail_500::cpp_regex_traits_base<char>, boost::re_detail_500::cpp_regex_traits_implementation<char> >::get(boost::re_detail_500::cpp_regex_traits_base<char> const&, unsigned long) in main-f41f28.o
boost::cpp_regex_traits<char>::get_catalog_name() in main-f41f28.o
boost::re_detail_500::get_mem_block() in main-f41f28.o
boost::re_detail_500::perl_matcher<std::__1::__wrap_iter<char const*="">, std:👎:allocator<boost::sub_match<std::__1::__wrap_iter<char const*=""> > >, boost::regex_traits<char, boost::cpp_regex_traits<char=""> > >::unwind_extra_block(bool) in main-f41f28.o
boost::re_detail_500::save_state_init::~save_state_init() in main-f41f28.o
"boost::scoped_static_mutex_lock::~scoped_static_mutex_lock()", referenced from:
boost::object_cache<boost::re_detail_500::cpp_regex_traits_base<char>, boost::re_detail_500::cpp_regex_traits_implementation<char> >::get(boost::re_detail_500::cpp_regex_traits_base<char> const&, unsigned long) in main-f41f28.o
boost::cpp_regex_traits<char>::get_catalog_name() in main-f41f28.o
boost::re_detail_500::get_mem_block() in main-f41f28.o
boost::re_detail_500::perl_matcher<std::__1::__wrap_iter<char const*="">, std:👎:allocator<boost::sub_match<std::__1::__wrap_iter<char const*=""> > >, boost::regex_traits<char, boost::cpp_regex_traits<char=""> > >::unwind_extra_block(bool) in main-f41f28.o
boost::re_detail_500::save_state_init::~save_state_init() in main-f41f28.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sdsorter] Error 1</char,></boost::sub_match<std::__1::__wrap_iter<char></std::__1::__wrap_iter<char></char></char></char></boost::re_detail_500::cpp_regex_traits_base<char></char,></boost::sub_match<std::__1::__wrap_iter<char></std::__1::__wrap_iter<char></char></char></char></boost::re_detail_500::cpp_regex_traits_base<char>

[David Koes]

As you undoubtedly realize from reading the error messages, there is a mismatch in the version of the operating system you are building for and the version your installed libraries are built for. What version of MacOS are you running? How did you install these libraries?

[Sherif Elsabbagh]

i have Big sur 11.5.2

i install these libraries using homebrew and conda

[Sherif Elsabbagh]

sorry for all these questions but I cant find any other alternative to this tool

[Sherif Elsabbagh]

Hi again.. I managed to find another tool called sdsort

but when i use it I have a txt file like this
REC minimizedAffinity
001 -10.807 0.000
002 -10.192 0.000
003 -10.044 0.000
004 -10.043 0.000
005 -9.874 0.000
006 -9.844 0.000
007 -9.796 0.000
008 -9.742 0.000
009 -9.698 0.000
010 -9.671 0.000
011 -9.567 0.000
012 -9.490 0.000
013 -9.449 0.000
014 -9.430 0.000
015 -9.407 0.000
016 -9.392 0.000
017 -9.280 0.000
018 -9.102 0.000
019 -9.098 0.000
020 C -9.088 0.000
021 C077 -9.066 0.000
022 -9.064 0.000
023 -9.060 0.000
024 -9.036 0.000
025 -9.019 0.000
026 -8.840 0.000
027 -8.813 0.000
028 -8.790 0.000
029 -8.789 0.000
030 -8.655 0.000

i tried to draw ROC using R but i got this result
Error in roc.default(grepl("active", d$TITLE), d$minimizedAffinity, direction = ">"): 'response' must have two levels
Traceback:

1. roc(grepl("active", d$TITLE), d$minimizedAffinity, direction = ">")
2. roc.default(grepl("active", d$TITLE), d$minimizedAffinity, direction = ">")
3. stop("'response' must have two levels")

[David Koes]

Your input files had mixed number of columns. I can't help with R issues.

I suspect you installed the various libraries prior to upgrading your operating system and you need to update them with homebrew/conda.

[David Koes]

I've uploaded an updated MacOS binary. See if it works for you.