rosetta building “zlib1g-dev” error

[Anonymous]

Hello

I am trying to build rosetta upon unbuntu (Oracle VM Virtual Box) with gcc (4.4.5) g++ (4.4.5) python (2.2.6). While trying to build rosetta with the command “scons bin” I got an error “usr/bin/Id: -lz not found”. I tried to install this library with command “sudo apt-get install zlib-dev” but got the following error.

jamil@jamil-VirtualBox:~/rosetta/rosetta_source$ sudo apt-get install zlib-dev
Reading package lists… Done
Building dependency tree
Reading state information… Done
Package zlib-dev is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package ‘zlib-dev’ has no installation candidate

Then I used the command “sudo spt-get install zlib1g-dev” after which library was installed. Again typing the same command gives:

jamil@jamil-VirtualBox:~/rosetta/rosetta_source$ sudo apt-get install zlib1g-dev
Reading package lists… Done
Building dependency tree
Reading state information… Done
zlib1g-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 267 not upgraded.

which I assume means that zlib library is installed. Now when I try to build rosetta (scons bin). It gives the following error (the first and the few end lines of the error is pasted in last)

scons: Reading SConscript files …
sh: svnversion: not found
sh: svn: not found

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File “/home/jamil/rosetta/rosetta_source/SConscript”, line 40, in
scons: done reading SConscript files.
scons: Building targets …
g++ -o build/src/debug/linux/2.6/32/x86/gcc/libcore.so -shared build/src/debug/linux/2.6/32/x86/gcc/core/init.os build/src/debug/linux/2.6/32/x86/gcc/core/svn_version.os build/src……………………..Lexternal/lib -Lbuild/src/debug/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lnumeric -lutility -lObjexxFCL -lz
collect2: ld terminated with signal 9 [Killed]
scons: *** [build/src/debug/linux/2.6/32/x86/gcc/libcore.so] Error 1
scons: building terminated because of errors

Please kindly suggest me how to solve this problem?

[Anonymous]

Unfortunately this isn’t quite the right information I need to diagnose the error – can you paste another line or three of what’s at the end? “ld terminated with signal 9” sounds like you killed it manually…

The errors at the beginning – svn is irrelevant, and all of the scons warnings are due to a mismatch between python and scons version.

[Anonymous]

here is the bigger chunk of error. It gave error by itself, I didnt killed it, However I overrode the user.settings as overrides” : {
“cc” : “gcc”,
“cxx” : “g++”,
},

error chunk from last is

build/src/debug/linux/2.6/32/x86/gcc/core/sequence/L1ScoringScheme.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/DPScoringScheme.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/PairScoringScheme.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/ProfSimScoringScheme.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/CompassScoringScheme.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/CompositeScoringScheme.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/ChemicalShiftScoringScheme.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/ScoringSchemeFactory.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/Sequence.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/SequenceAlignment.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/SequenceMapping.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/SequenceProfile.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/CompositeSequence.os build/src/debug/linux/2.6/32/x86/gcc/core/sequence/ChemicalShiftSequence.os build/src/debug/linux/2.6/32/x86/gcc/core/options/after_opts.os build/src/debug/linux/2.6/32/x86/gcc/core/options/option.os build/src/debug/linux/2.6/32/x86/gcc/core/options/util.os build/src/debug/linux/2.6/32/x86/gcc/core/fragment/picking_old/vall/util.os build/src/debug/linux/2.6/32/x86/gcc/core/fragment/picking_old/vall/vall_io.os build/src/debug/linux/2.6/32/x86/gcc/core/fragment/picking_old/vall/VallLibrarian.os build/src/debug/linux/2.6/32/x86/gcc/core/fragment/picking_old/vall/VallResidue.os -Llib -Lexternal/lib -Lbuild/src/debug/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lnumeric -lutility -lObjexxFCL -lz
collect2: ld terminated with signal 9 [Killed]
scons: *** [build/src/debug/linux/2.6/32/x86/gcc/libcore.so] Error 1
scons: building terminated because of errors.

Any thoughts??

[Anonymous]

Thankyou so much smlewis, I compiled it in release mode and its done… thanks again….

Install file: “build/src/release/linux/2.6/32/x86/gcc/super_aln.default.linuxgccrelease” as “bin/super_aln.default.linuxgccrelease”
g++ -o build/src/release/linux/2.6/32/x86/gcc/super_aln.linuxgccrelease -Wl,-rpath=/home/jamil/rosetta/rosetta_source/build/src/release/linux/2.6/32/x86/gcc/ build/src/release/linux/2.6/32/x86/gcc/apps/public/comparative_modeling/super_aln.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -ldevel -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
Install file: “build/src/release/linux/2.6/32/x86/gcc/super_aln.linuxgccrelease” as “bin/super_aln.linuxgccrelease”
scons: done building targets.

[Anonymous]

Looking at it further, I realize you’re building in debug instead of release. I assume you want the (faster, lighter) release build rather than the debugging build. I don’t know what’s causing it to crash, but one possibility with debug mode is that you’re running out of memory during compiling (compiling in debug requires something like 2GB). Googling signal 9 for ld indicates it might be a memory quantity issue.

To compile in release mode, add mode=release to your command line (scons bin mode=release -j#), where # is the number of processors you can afford. It will restart the compile from the beginning, unfortunately.

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