Hello,
I am attempting to install lastz and yasra for plastid genome assembly, but am having problems. I downloaded lastz here:
and yasra v1 here:
I was informed by the user that they needed yasra v1 as later versions are not compatible with their pipeline. Anyway, I downloaded yasra first, but it didn't want to install, so I moved on to lastz. I issued:
sudo make
which produced some errors. I googled a bit, and found a thread here on seqanswers where it was suggested to go into the lastz makefile, and delete -Werror from line 31, and repeat install. It worked!
But then I tried to install yasra and it seems it is dependent on -Werror:
sudo make
make pipeline
make[1]: Entering directory `/bin/yasra'
gcc -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror -Wno-unused-variable -Wunused-parameter -Wreturn-type -Wpointer-arith -Wswitch -Wcast-align -Winline -Wnested-externs -Wextra -DNDEBUG -O2 -funroll-all-loops -minline-all-stringops -momit-leaf-frame-pointer -I. -c -o substitutions.o substitutions.c
substitutions.c: In function ‘main’:
substitutions.c:35:52: error: variable ‘match’ set but not used [-Werror=unused-but-set-variable]
substitutions.c:34:7: error: variable ‘old_seq_name’ set but not used [-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors
make[1]: *** [substitutions.o] Error 1
make[1]: Leaving directory `/bin/yasra'
make: *** [all] Error 2
I am doing all of this in my /bin directory since I can't seem to get new directories added permanently to my path (I only seem to know enough to cause trouble for myself and others), which is why I am using sudo with each command. I thought perhaps directory permissions were really the cause of my trouble, so I moved the lastz folder to my desktop and repeated the make command, but got the same problem output:
sudo make
cd src && make lastz lastz_D
make[1]: Entering directory `/home/enggen/Downloads/lastz-distrib-1.02.00/src'
gcc -c -O3 -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DVERSION_MAJOR="\"1"\" -DVERSION_MINOR="\"02"\" -DVERSION_SUBMINOR="\"00"\" -DREVISION_DATE="\"20100112"\" -DSUBVERSION_REV="\"1278:1279M"\" -Dscore_type=\'I\' lastz.c -o lastz.o
lastz.c: In function ‘main’:
lastz.c:441:9: error: variable ‘freeTargetRev’ set but not used [-Werror=unused-but-set-variable]
lastz.c: In function ‘start_one_strand’:
lastz.c:1669:9: error: variable ‘base****’ set but not used [-Werror=unused-but-set-variable]
lastz.c: In function ‘parse_options’:
lastz.c:5048:9: error: variable ‘seq1Filename’ set but not used [-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors
make[1]: *** [lastz.o] Error 1
make[1]: Leaving directory `/home/enggen/Downloads/lastz-distrib-1.02.00/src'
make: *** [build_lastz] Error 2
I am running 64bit Ubuntu 12.04, which may or may not place certain files in the same place as other linux distros.
Any ideas how to solve these problems?
I am attempting to install lastz and yasra for plastid genome assembly, but am having problems. I downloaded lastz here:
and yasra v1 here:
I was informed by the user that they needed yasra v1 as later versions are not compatible with their pipeline. Anyway, I downloaded yasra first, but it didn't want to install, so I moved on to lastz. I issued:
sudo make
which produced some errors. I googled a bit, and found a thread here on seqanswers where it was suggested to go into the lastz makefile, and delete -Werror from line 31, and repeat install. It worked!
But then I tried to install yasra and it seems it is dependent on -Werror:
sudo make
make pipeline
make[1]: Entering directory `/bin/yasra'
gcc -W -Wformat -Wimplicit -Wreturn-type -Wall -Werror -Wno-unused-variable -Wunused-parameter -Wreturn-type -Wpointer-arith -Wswitch -Wcast-align -Winline -Wnested-externs -Wextra -DNDEBUG -O2 -funroll-all-loops -minline-all-stringops -momit-leaf-frame-pointer -I. -c -o substitutions.o substitutions.c
substitutions.c: In function ‘main’:
substitutions.c:35:52: error: variable ‘match’ set but not used [-Werror=unused-but-set-variable]
substitutions.c:34:7: error: variable ‘old_seq_name’ set but not used [-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors
make[1]: *** [substitutions.o] Error 1
make[1]: Leaving directory `/bin/yasra'
make: *** [all] Error 2
I am doing all of this in my /bin directory since I can't seem to get new directories added permanently to my path (I only seem to know enough to cause trouble for myself and others), which is why I am using sudo with each command. I thought perhaps directory permissions were really the cause of my trouble, so I moved the lastz folder to my desktop and repeated the make command, but got the same problem output:
sudo make
cd src && make lastz lastz_D
make[1]: Entering directory `/home/enggen/Downloads/lastz-distrib-1.02.00/src'
gcc -c -O3 -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DVERSION_MAJOR="\"1"\" -DVERSION_MINOR="\"02"\" -DVERSION_SUBMINOR="\"00"\" -DREVISION_DATE="\"20100112"\" -DSUBVERSION_REV="\"1278:1279M"\" -Dscore_type=\'I\' lastz.c -o lastz.o
lastz.c: In function ‘main’:
lastz.c:441:9: error: variable ‘freeTargetRev’ set but not used [-Werror=unused-but-set-variable]
lastz.c: In function ‘start_one_strand’:
lastz.c:1669:9: error: variable ‘base****’ set but not used [-Werror=unused-but-set-variable]
lastz.c: In function ‘parse_options’:
lastz.c:5048:9: error: variable ‘seq1Filename’ set but not used [-Werror=unused-but-set-variable]
cc1: all warnings being treated as errors
make[1]: *** [lastz.o] Error 1
make[1]: Leaving directory `/home/enggen/Downloads/lastz-distrib-1.02.00/src'
make: *** [build_lastz] Error 2
I am running 64bit Ubuntu 12.04, which may or may not place certain files in the same place as other linux distros.
Any ideas how to solve these problems?
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