STAR installation make error
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7.5 years ago
jolin0701-dy ▴ 100

I'd like to install STAR in our cluster.

I download the .tar.gz files and tar -xvf this file.

$cd source
$make STAR
Makefile:71: Depend.list: No such file or directory
make: Warning: File `parametersDefault.xxd' has modification time 9.5e+03 s in the future
make -C htslib lib-static
make[1]: Entering directory `/home/oasis/gordon-data/NGS-ann-project-new/apps/STAR/source/htslib'
make[1]: Warning: File `kfunc.o' has modification time 9.5e+03 s in the future
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c
In file included from bgzf.c:38:
htslib/bgzf.h:33:18: error: zlib.h: No such file or directory
In file included from bgzf.c:38:
htslib/bgzf.h:59: error: expected specifier-qualifier-list before ‘z_stream’
bgzf.c: In function ‘bgzf_write_init’:
bgzf.c:140: error: ‘Z_DEFAULT_COMPRESSION’ undeclared (first use in this function)
bgzf.c:140: error: (Each undeclared identifier is reported only once
bgzf.c:140: error: for each function it appears in.)
bgzf.c: In function ‘bgzf_open’:
bgzf.c:158: warning: implicit declaration of function ‘compressBound’
bgzf.c: In function ‘bgzf_compress’:
bgzf.c:219: error: ‘z_stream’ undeclared (first use in this function)
bgzf.c:219: error: expected ‘;’ before ‘zs’
bgzf.c:223: error: ‘zs’ undeclared (first use in this function)
bgzf.c:224: error: ‘Bytef’ undeclared (first use in this function)
bgzf.c:224: error: expected expression before ‘)’ token
bgzf.c:228: warning: implicit declaration of function ‘deflateInit2’
bgzf.c:228: error: ‘Z_DEFLATED’ undeclared (first use in this function)
bgzf.c:228: error: ‘Z_DEFAULT_STRATEGY’ undeclared (first use in this function)
bgzf.c:228: error: ‘Z_OK’ undeclared (first use in this function)
bgzf.c:229: warning: implicit declaration of function ‘deflate’
bgzf.c:229: error: ‘Z_FINISH’ undeclared (first use in this function)
bgzf.c:229: error: ‘Z_STREAM_END’ undeclared (first use in this function)
bgzf.c:230: warning: implicit declaration of function ‘deflateEnd’
bgzf.c:236: warning: implicit declaration of function ‘crc32’
bgzf.c:236: error: expected expression before ‘)’ token
bgzf.c: In function ‘inflate_block’:
bgzf.c:257: error: ‘z_stream’ undeclared (first use in this function)
bgzf.c:257: error: expected ‘;’ before ‘zs’
bgzf.c:258: error: ‘zs’ undeclared (first use in this function)
bgzf.c:260: error: ‘Bytef’ undeclared (first use in this function)
bgzf.c:260: error: expected expression before ‘)’ token
bgzf.c:262: error: expected expression before ‘)’ token
bgzf.c:265: warning: implicit declaration of function ‘inflateInit2’
bgzf.c:265: error: ‘Z_OK’ undeclared (first use in this function)
bgzf.c:269: warning: implicit declaration of function ‘inflate’
bgzf.c:269: error: ‘Z_FINISH’ undeclared (first use in this function)
bgzf.c:269: error: ‘Z_STREAM_END’ undeclared (first use in this function)
bgzf.c:270: warning: implicit declaration of function ‘inflateEnd’
bgzf.c: In function ‘inflate_gzip_block’:
bgzf.c:283: error: ‘Z_OK’ undeclared (first use in this function)
bgzf.c:286: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:288: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:289: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:289: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:290: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:291: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:296: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:296: error: ‘Bytef’ undeclared (first use in this function)
bgzf.c:296: error: expected expression before ‘)’ token
bgzf.c:297: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:298: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:298: error: ‘Z_NO_FLUSH’ undeclared (first use in this function)
bgzf.c:300: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:303: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:305: error: ‘Z_STREAM_END’ undeclared (first use in this function)
bgzf.c:306: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c: In function ‘bgzf_read_block’:
bgzf.c:467: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:467: error: ‘z_stream’ undeclared (first use in this function)
bgzf.c:467: error: expected expression before ‘)’ token
bgzf.c:468: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:469: error: ‘Z_OK’ undeclared (first use in this function)
bgzf.c:474: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:475: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c: In function ‘bgzf_close’:
bgzf.c:778: error: ‘BGZF’ has no member named ‘gz_stream’
bgzf.c:779: error: ‘BGZF’ has no member named ‘gz_stream’
make[1]: *** [bgzf.o] Error 1
make[1]: Leaving directory `/home/oasis/gordon-data/NGS-ann-project-new/apps/STAR/source/htslib'
make: *** [htslib/libhts.a] Error 2

Any help would be greatly appreciated~~
software error • 5.1k views
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1
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I'd wonder if it may make more sense to install the Anaconda package manager and then install STAR using that?

The command then would be conda install -c bioconda star.

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0
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Thanks for your reply. I prefer to install it from scratch, since I use linux cluster....

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please, send a longer stack trace.

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error: zlib.h: No such file or directory

Either missing Zlib-devel or they are not in your library paths.

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2
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7.5 years ago

: error: zlib.h: No such file or directory

install libz :

sudo apt-get install libz-dev
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0
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some errors during sudo apt-get install libz-dev

 $ sudo apt-get install libz-dev
    Reading package lists... Done
    Building dependency tree       
    Reading state information... Done
    Note, selecting 'zlib1g-dev' instead of 'libz-dev'
    The following NEW packages will be installed:
      zlib1g-dev
    0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
    Need to get 192 kB of archives.
    After this operation, 446 kB of additional disk space will be used.
    WARNING: The following packages cannot be authenticated!
      zlib1g-dev
    Install these packages without verification [y/N]? y
    Err http://ftp.us.debian.org/debian/ squeeze/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3
      404  Not Found [IP: 64.50.236.52 80]
    Failed to fetch http://ftp.us.debian.org/debian/pool/main/z/zlib/zlib1g-dev_1.2.3.4.dfsg-3_amd64.deb  404  Not Found [IP: 64.50.236.52 80]
    E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

    $ sudo apt-get install libz-dev --fix-missing
    Reading package lists... Done
    Building dependency tree       
    Reading state information... Done
    Note, selecting 'zlib1g-dev' instead of 'libz-dev'
    The following NEW packages will be installed:
      zlib1g-dev
    0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
    Need to get 192 kB of archives.
    After this operation, 446 kB of additional disk space will be used.
    WARNING: The following packages cannot be authenticated!
      zlib1g-dev
    Install these packages without verification [y/N]? y
    Err http://ftp.us.debian.org/debian/ squeeze/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3
      404  Not Found [IP: 64.50.233.100 80]
    Failed to fetch http://ftp.us.debian.org/debian/pool/main/z/zlib/zlib1g-dev_1.2.3.4.dfsg-3_amd64.deb  404  Not Found [IP: 64.50.233.100 80]
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Not Found [IP: 64.50.233.100 80]

working behind a proxy ? https://askubuntu.com/questions/89437/how-to-install-packages-with-apt-get-on-a-system-connected-via-proxy

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Yea, thats likely the problem. Consult your clouds documentation and see if theres a proxy. If there is you have to set an environment variable to the proxy (eg., export ftp_proxy=0.0.0.0), then pass the users env to sudo. So: export ftp_proxy=0.0.0.0 sudo -E apt-get install ....

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also, the github for STAR comes with precompiled binaries. you could always use those too.

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