Question: STAR installation make error
0
gravatar for jolin0701-dy
21 months ago by
jolin0701-dy70
jolin0701-dy70 wrote:

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 • 1.1k views
ADD COMMENTlink modified 21 months ago by Pierre Lindenbaum118k • written 21 months ago by jolin0701-dy70
1

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.

ADD REPLYlink written 21 months ago by Sinji2.8k

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

ADD REPLYlink written 21 months ago by jolin0701-dy70

please, send a longer stack trace.

ADD REPLYlink written 21 months ago by Pierre Lindenbaum118k

error: zlib.h: No such file or directory

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

ADD REPLYlink written 21 months ago by genomax64k
1
gravatar for Pierre Lindenbaum
21 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

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

install libz :

sudo apt-get install libz-dev
ADD COMMENTlink written 21 months ago by Pierre Lindenbaum118k

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]
ADD REPLYlink modified 21 months ago • written 21 months ago by jolin0701-dy70

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

ADD REPLYlink written 21 months ago by Pierre Lindenbaum118k

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 ....

ADD REPLYlink written 21 months ago by mforde841.2k

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

ADD REPLYlink written 21 months ago by mforde841.2k
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