problem2 with install on linux

mothur bugs
1

in continuation of the previous post: problem with install on linux

I tried to install mothur on ubuntu 12 and after command “make” saw new error:

collect2: error: ld returned 1 exit status
makefile:110: Recipe executions cause an error for «mothur»
make: *** [mothur] Error 1

How could I resolve this problem?

thanks!

2

Have you tried our Mothur.cen_64.noOpt.zip version for Linux? https://github.com/mothur/mothur/releases/tag/v1.36.1

If you are compiling with boost, do you have zlib.cpp and gzip.cpp in the source folder for mothur? Can you try compiling with this makefile?

###################################################
#
# Makefile for mothur
#
###################################################

#
# Macros
#

64BIT_VERSION ?= yes
USEREADLINE ?= yes
USEBOOST ?= yes
MOTHUR_FILES="\"Enter_your_default_path_here\""
RELEASE_DATE = "\"1/13/2016\""
VERSION = "\"1.36.1\""

ifeq  ($(strip $(64BIT_VERSION)),yes)
    CXXFLAGS += -DBIT_VERSION
endif


CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}

ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
else
    CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
endif


# if you do not want to use the readline library, set this to no.
# make sure you have the library installed


ifeq  ($(strip $(USEREADLINE)),yes)
    CXXFLAGS += -DUSE_READLINE
    LIBS += -lreadline
endif


#The boost libraries allow you to read gz files.
ifeq  ($(strip $(USEBOOST)),yes)
    LIBS += -lboost_iostreams
endif

#
# INCLUDE directories for mothur
#
#
    VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/metastats:source/randomforest:source/read:source/svm
    skipUchime := source/uchime_src/
    subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))
    subDirIncludes = $(patsubst %, -I %, $(subdirs))
    subDirLinking =  $(patsubst %, -L%, $(subdirs))
    CXXFLAGS += -I. $(subDirIncludes)
    LDFLAGS += $(subDirLinking)


#
# Get the list of all .cpp files, rename to .o files
#
    OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
    OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
    OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
    OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))

mothur : $(OBJECTS) uchime
 $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)

uchime:
    cd source/uchime_src && ./mk && mv uchime ../../ && cd ..

install : mothur

%.o : %.c %.h
 $(COMPILE.c) $(OUTPUT_OPTION) $<
%.o : %.cpp %.h
 $(COMPILE.cpp) $(OUTPUT_OPTION) $<
%.o : %.cpp %.hpp
 $(COMPILE.cpp) $(OUTPUT_OPTION) $<

clean :
 @rm -f $(OBJECTS)
 @rm -f uchime