not sure what I can do about this...

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Re: not sure what I can do about this...

Peter Cock
Sorry Edgar,

It looks like something else is causing this error (and my guess
about different versions of Linux on Galaxy and the cluster was
wrong):

ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
undefined symbol: gzopen64

It may be important how the pysam wheel was compiled, perhaps
Nate may be able to comment (CC'd).

Peter

On Wed, May 25, 2016 at 12:40 PM, Fernandez Edgar
<[hidden email]> wrote:
> Hello Peter,
>
> For now, my new installation of galaxy v16.01 is on one test desktop running Oracle Linux 6.
> Before changing my production installation, I'm doing my due diligent.
>
> Let me know what you think...
>
> Edgar Fernandez
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Re: not sure what I can do about this...

fernandez Edgar

Hey guys,

 

I believe I figure it out.

The problem is my Oracle Linux 6 repository slowness of updates.

 

I have libz 1.2.3 installed and that version is missing gzopen64.

However, the version 1.2.8 exists and is not out for oracle.

 

Here is what I did to find and please pay attention to the colored code :

 

[root@gavroche] [08:59:24] [/tmp] [39 files - 8.0Mb]

[0]# ldd /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so

        linux-vdso.so.1 =>  (0x00007ffd4cfad000)

        libz.so.1 => /lib64/libz.so.1 (0x00007f4435cf2000)

        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4435ad5000)

        libc.so.6 => /lib64/libc.so.6 (0x00007f4435740000)

        /lib64/ld-linux-x86-64.so.2 (0x00000033ef400000)

 

[root@gavroche] [08:59:29] [/tmp] [39 files - 8.0Mb]

[0]# ls -al /lib64/libz.so.1

lrwxrwxrwx. 1 root root 13 Oct 22  2014 /lib64/libz.so.1 -> libz.so.1.2.3

 

[root@gavroche] [08:59:34] [/tmp] [39 files - 8.0Mb]

[0]# ldd /lib64/libz.so.1.2.3

        linux-vdso.so.1 =>  (0x00007ffd9dcce000)

        libc.so.6 => /lib64/libc.so.6 (0x00000033ef800000)

        /lib64/ld-linux-x86-64.so.2 (0x00000033ef400000)

 

[root@gavroche] [09:00:02] [/tmp] [39 files - 8.0Mb]

[0]# readelf -a /lib64/libz.so.1.2.3

ELF Header:

  Magic:   7f 45 4c 46 02 01 01 00 00 00 00 00 00 00 00 00

  Class:                             ELF64

  Data:                              2's complement, little endian

  Version:                           1 (current)

  OS/ABI:                            UNIX - System V

  ABI Version:                       0

  Type:                              DYN (Shared object file)

  Machine:                           Advanced Micro Devices X86-64

  Version:                           0x1

  Entry point address:               0x33f0802120

  Start of program headers:          64 (bytes into file)

  Start of section headers:          89112 (bytes into file)

  Flags:                             0x0

  Size of this header:               64 (bytes)

  Size of program headers:           56 (bytes)

  Number of program headers:         7

  Size of section headers:           64 (bytes)

  Number of section headers:         31

  Section header string table index: 30

 

Section Headers:

  [Nr] Name              Type             Address           Offset

       Size              EntSize          Flags  Link  Info  Align

  [ 0]                   NULL             0000000000000000  00000000

       0000000000000000  0000000000000000           0     0     0

  [ 1] .note.gnu.build-i NOTE             00000033f08001c8  000001c8

       0000000000000024  0000000000000000   A       0     0     4

  [ 2] .gnu.hash         GNU_HASH         00000033f08001f0  000001f0

       00000000000002a8  0000000000000000   A       3     0     8

  [ 3] .dynsym           DYNSYM           00000033f0800498  00000498

       0000000000000a80  0000000000000018   A       4     2     8

  [ 4] .dynstr           STRTAB           00000033f0800f18  00000f18

       00000000000004c6  0000000000000000   A       0     0     1

  [ 5] .gnu.version      VERSYM           00000033f08013de  000013de

       00000000000000e0  0000000000000002   A       3     0     2

  [ 6] .gnu.version_d    VERDEF           00000033f08014c0  000014c0

       00000000000000ec  0000000000000000   A       4     7     8

  [ 7] .gnu.version_r    VERNEED          00000033f08015b0  000015b0

       0000000000000040  0000000000000000   A       4     1     8

  [ 8] .rela.dyn         RELA             00000033f08015f0  000015f0

       0000000000000330  0000000000000018   A       3     0     8

  [ 9] .rela.plt         RELA             00000033f0801920  00001920

       00000000000004b0  0000000000000018   A       3    11     8

  [10] .init             PROGBITS         00000033f0801dd0  00001dd0

       0000000000000018  0000000000000000  AX       0     0     4

  [11] .plt              PROGBITS         00000033f0801de8  00001de8

       0000000000000330  0000000000000010  AX       0     0     4

  [12] .text             PROGBITS         00000033f0802120  00002120

       000000000000b288  0000000000000000  AX       0     0     16

  [13] .fini             PROGBITS         00000033f080d3a8  0000d3a8

       000000000000000e  0000000000000000  AX       0     0     4

  [14] .rodata           PROGBITS         00000033f080d3c0  0000d3c0

       00000000000060be  0000000000000000   A       0     0     32

  [15] .eh_frame_hdr     PROGBITS         00000033f0813480  00013480

       00000000000002bc  0000000000000000   A       0     0     4

  [16] .eh_frame         PROGBITS         00000033f0813740  00013740

       0000000000000d34  0000000000000000   A       0     0     8

  [17] .ctors            PROGBITS         00000033f0a14cd8  00014cd8

       0000000000000010  0000000000000000  WA       0     0     8

  [18] .dtors            PROGBITS         00000033f0a14ce8  00014ce8

       0000000000000010  0000000000000000  WA       0     0     8

  [19] .jcr              PROGBITS         00000033f0a14cf8  00014cf8

       0000000000000008  0000000000000000  WA       0     0     8

  [20] .data.rel.ro      PROGBITS         00000033f0a14d00  00014d00

       00000000000000f8  0000000000000000  WA       0     0     32

  [21] .dynamic          DYNAMIC          00000033f0a14df8  00014df8

       00000000000001b0  0000000000000010  WA       4     0     8

  [22] .got              PROGBITS         00000033f0a14fa8  00014fa8

       0000000000000040  0000000000000008  WA       0     0     8

  [23] .got.plt          PROGBITS         00000033f0a14fe8  00014fe8

       00000000000001a8  0000000000000008  WA       0     0     8

  [24] .data             PROGBITS         00000033f0a151a0  000151a0

       0000000000000060  0000000000000000  WA       0     0     32

  [25] .bss              NOBITS           00000033f0a15200  00015200

       0000000000000010  0000000000000000  WA       0     0     8

  [26] .gnu_debuglink    PROGBITS         0000000000000000  00015200

       0000000000000018  0000000000000000           0     0     4

  [27] .gnu.liblist      GNU_LIBLIST      0000000000000000  00015218

       0000000000000028  0000000000000014          28     0     4

  [28] .gnu.libstr       STRTAB           0000000000000000  00015240

       0000000000000027  0000000000000000           0     0     1

  [29] .gnu.prelink_undo PROGBITS         0000000000000000  00015268

       0000000000000888  0000000000000001           0     0     8

  [30] .shstrtab         STRTAB           0000000000000000  00015af0

       0000000000000125  0000000000000000           0     0     1

Key to Flags:

  W (write), A (alloc), X (execute), M (merge), S (strings)

  I (info), L (link order), G (group), x (unknown)

  O (extra OS processing required) o (OS specific), p (processor specific)

 

There are no section groups in this file.

 

Program Headers:

  Type           Offset             VirtAddr           PhysAddr

                 FileSiz            MemSiz              Flags  Align

  LOAD           0x0000000000000000 0x00000033f0800000 0x00000033f0800000

                 0x0000000000014474 0x0000000000014474  R E    200000

  LOAD           0x0000000000014cd8 0x00000033f0a14cd8 0x00000033f0a14cd8

                 0x0000000000000528 0x0000000000000538  RW     200000

  DYNAMIC        0x0000000000014df8 0x00000033f0a14df8 0x00000033f0a14df8

                 0x00000000000001b0 0x00000000000001b0  RW     8

  NOTE           0x00000000000001c8 0x00000033f08001c8 0x00000033f08001c8

                 0x0000000000000024 0x0000000000000024  R      4

  GNU_EH_FRAME   0x0000000000013480 0x00000033f0813480 0x00000033f0813480

                 0x00000000000002bc 0x00000000000002bc  R      4

  GNU_STACK      0x0000000000000000 0x0000000000000000 0x0000000000000000

                 0x0000000000000000 0x0000000000000000  RW     8

  GNU_RELRO      0x0000000000014cd8 0x00000033f0a14cd8 0x00000033f0a14cd8

                 0x0000000000000328 0x0000000000000328  R      1

 

Section to Segment mapping:

  Segment Sections...

   00     .note.gnu.build-id .gnu.hash .dynsym .dynstr .gnu.version .gnu.version_d .gnu.version_r .rela.dyn .rela.plt .init .plt .text .fini .rodata .eh_frame_hdr .eh_frame

   01     .ctors .dtors .jcr .data.rel.ro .dynamic .got .got.plt .data .bss

   02     .dynamic

   03     .note.gnu.build-id

   04     .eh_frame_hdr

   05

   06     .ctors .dtors .jcr .data.rel.ro .dynamic .got

 

Dynamic section at offset 0x14df8 contains 25 entries:

  Tag        Type                         Name/Value

0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]

0x000000000000000e (SONAME)             Library soname: [libz.so.1]

0x000000000000000c (INIT)               0x33f0801dd0

0x000000000000000d (FINI)               0x33f080d3a8

0x000000006ffffef5 (GNU_HASH)           0x33f08001f0

0x0000000000000005 (STRTAB)             0x33f0800f18

0x0000000000000006 (SYMTAB)             0x33f0800498

0x000000000000000a (STRSZ)              1222 (bytes)

0x000000000000000b (SYMENT)             24 (bytes)

0x0000000000000003 (PLTGOT)             0x33f0a14fe8

0x0000000000000002 (PLTRELSZ)           1200 (bytes)

0x0000000000000014 (PLTREL)             RELA

0x0000000000000017 (JMPREL)             0x33f0801920

0x0000000000000007 (RELA)               0x33f08015f0

0x0000000000000008 (RELASZ)             816 (bytes)

0x0000000000000009 (RELAENT)            24 (bytes)

0x000000006ffffffc (VERDEF)             0x33f08014c0

0x000000006ffffffd (VERDEFNUM)          7

0x000000006ffffffe (VERNEED)            0x33f08015b0

0x000000006fffffff (VERNEEDNUM)         1

0x000000006ffffff0 (VERSYM)             0x33f08013de

0x000000006ffffff9 (RELACOUNT)          26

0x000000006ffffdf8 (CHECKSUM)           0xb158153e

0x000000006ffffdf5 (GNU_PRELINKED)      2016-02-23T09:02:06

0x0000000000000000 (NULL)               0x0

 

Relocation section '.rela.dyn' at offset 0x15f0 contains 34 entries:

  Offset          Info           Type           Sym. Value    Sym. Name + Addend

0033f0a14d08  000000000008 R_X86_64_RELATIVE                    00000033f0805940

0033f0a14d18  000000000008 R_X86_64_RELATIVE                    00000033f0805540

0033f0a14d28  000000000008 R_X86_64_RELATIVE                    00000033f0805540

0033f0a14d38  000000000008 R_X86_64_RELATIVE                    00000033f0805540

0033f0a14d48  000000000008 R_X86_64_RELATIVE                    00000033f0804ff0

0033f0a14d58  000000000008 R_X86_64_RELATIVE                    00000033f0804ff0

0033f0a14d68  000000000008 R_X86_64_RELATIVE                    00000033f0804ff0

0033f0a14d78  000000000008 R_X86_64_RELATIVE                    00000033f0804ff0

0033f0a14d88  000000000008 R_X86_64_RELATIVE                    00000033f0804ff0

0033f0a14d98  000000000008 R_X86_64_RELATIVE                    00000033f0804ff0

0033f0a14da0  000000000008 R_X86_64_RELATIVE                    00000033f0811eac

0033f0a14da8  000000000008 R_X86_64_RELATIVE                    00000033f0811ebc

0033f0a14db0  000000000008 R_X86_64_RELATIVE                    00000033f080d3c5

0033f0a14db8  000000000008 R_X86_64_RELATIVE                    00000033f0811ec7

0033f0a14dc0  000000000008 R_X86_64_RELATIVE                    00000033f0811ed2

0033f0a14dc8  000000000008 R_X86_64_RELATIVE                    00000033f0811edf

0033f0a14dd0  000000000008 R_X86_64_RELATIVE                    00000033f0811eea

0033f0a14dd8  000000000008 R_X86_64_RELATIVE                    00000033f0811efe

0033f0a14de0  000000000008 R_X86_64_RELATIVE                    00000033f0811f0b

0033f0a14de8  000000000008 R_X86_64_RELATIVE                    00000033f080d3c5

0033f0a14df0  000000000008 R_X86_64_RELATIVE                    00000033f0a14df0

0033f0a151a0  000000000008 R_X86_64_RELATIVE                    00000033f0811740

0033f0a151a8  000000000008 R_X86_64_RELATIVE                    00000033f0811c60

0033f0a151c0  000000000008 R_X86_64_RELATIVE                    00000033f0811bc0

0033f0a151c8  000000000008 R_X86_64_RELATIVE                    00000033f0811d60

0033f0a151e8  000000000008 R_X86_64_RELATIVE                    00000033f0811e60

0033f0a14fa8  000500000006 R_X86_64_GLOB_DAT 0000000000000000 __gmon_start__ + 0

0033f0a14fb0  000600000006 R_X86_64_GLOB_DAT 0000000000000000 _Jv_RegisterClasses + 0

0033f0a14fb8  004d00000006 R_X86_64_GLOB_DAT 00000033f0808da0 zcalloc + 0

0033f0a14fc0  000f00000006 R_X86_64_GLOB_DAT 0000000000000000 __cxa_finalize + 0

0033f0a14fc8  005e00000006 R_X86_64_GLOB_DAT 00000033f0811640 _length_code + 0

0033f0a14fd0  003e00000006 R_X86_64_GLOB_DAT 00000033f0811440 _dist_code + 0

0033f0a14fd8  003f00000006 R_X86_64_GLOB_DAT 00000033f0a14da0 z_errmsg + 0

0033f0a14fe0  005400000006 R_X86_64_GLOB_DAT 00000033f0808d90 zcfree + 0

 

Relocation section '.rela.plt' at offset 0x1920 contains 50 entries:

  Offset          Info           Type           Sym. Value    Sym. Name + Addend

0033f0a15000  001e00000007 R_X86_64_JUMP_SLO 00000033f0807d10 _tr_align + 0

0033f0a15008  004800000007 R_X86_64_JUMP_SLO 00000033f0808db0 inflateReset + 0

0033f0a15010  000200000007 R_X86_64_JUMP_SLO 0000000000000000 memset + 0

0033f0a15018  000300000007 R_X86_64_JUMP_SLO 0000000000000000 ftell + 0

0033f0a15020  004f00000007 R_X86_64_JUMP_SLO 00000033f0807b70 _tr_stored_block + 0

0033f0a15028  005900000007 R_X86_64_JUMP_SLO 00000033f0808fd0 inflateEnd + 0

0033f0a15030  000400000007 R_X86_64_JUMP_SLO 0000000000000000 __fprintf_chk + 0

0033f0a15038  000700000007 R_X86_64_JUMP_SLO 0000000000000000 fseek + 0

0033f0a15040  002f00000007 R_X86_64_JUMP_SLO 00000033f0805b10 deflate + 0

0033f0a15048  006100000007 R_X86_64_JUMP_SLO 00000033f08032f0 gzrewind + 0

0033f0a15050  006900000007 R_X86_64_JUMP_SLO 00000033f0806c70 deflateInit_ + 0

0033f0a15058  000800000007 R_X86_64_JUMP_SLO 0000000000000000 malloc + 0

0033f0a15060  000900000007 R_X86_64_JUMP_SLO 0000000000000000 fopen + 0

0033f0a15068  006a00000007 R_X86_64_JUMP_SLO 00000033f0803b10 gzseek + 0

0033f0a15070  000a00000007 R_X86_64_JUMP_SLO 0000000000000000 __vsnprintf_chk + 0

0033f0a15078  002300000007 R_X86_64_JUMP_SLO 00000033f0808eb0 inflateInit2_ + 0

0033f0a15080  004600000007 R_X86_64_JUMP_SLO 00000033f08096f0 inflate + 0

0033f0a15088  000b00000007 R_X86_64_JUMP_SLO 0000000000000000 fputc + 0

0033f0a15090  000c00000007 R_X86_64_JUMP_SLO 0000000000000000 free + 0

0033f0a15098  004c00000007 R_X86_64_JUMP_SLO 00000033f0803180 gzwrite + 0

0033f0a150a0  000d00000007 R_X86_64_JUMP_SLO 0000000000000000 strlen + 0

0033f0a150a8  004700000007 R_X86_64_JUMP_SLO 00000033f0802680 compress2 + 0

0033f0a150b0  005300000007 R_X86_64_JUMP_SLO 00000033f0802780 crc32 + 0

0033f0a150b8  000e00000007 R_X86_64_JUMP_SLO 0000000000000000 ferror + 0

0033f0a150c0  005a00000007 R_X86_64_JUMP_SLO 00000033f08044f0 deflateEnd + 0

0033f0a150c8  000f00000007 R_X86_64_JUMP_SLO 0000000000000000 __cxa_finalize + 0

0033f0a150d0  006500000007 R_X86_64_JUMP_SLO 00000033f08067f0 deflateReset + 0

0033f0a150d8  001000000007 R_X86_64_JUMP_SLO 0000000000000000 fdopen + 0

0033f0a150e0  006e00000007 R_X86_64_JUMP_SLO 00000033f0806ca0 _tr_init + 0

0033f0a150e8  001100000007 R_X86_64_JUMP_SLO 0000000000000000 strerror + 0

0033f0a150f0  001200000007 R_X86_64_JUMP_SLO 0000000000000000 strcat + 0

0033f0a150f8  001300000007 R_X86_64_JUMP_SLO 0000000000000000 memcpy + 0

0033f0a15100  001400000007 R_X86_64_JUMP_SLO 0000000000000000 fread + 0

0033f0a15108  001500000007 R_X86_64_JUMP_SLO 0000000000000000 __errno_location + 0

0033f0a15110  001600000007 R_X86_64_JUMP_SLO 0000000000000000 __stack_chk_fail + 0

0033f0a15118  001700000007 R_X86_64_JUMP_SLO 0000000000000000 strcpy + 0

0033f0a15120  003600000007 R_X86_64_JUMP_SLO 00000033f0802660 compressBound + 0

0033f0a15128  005200000007 R_X86_64_JUMP_SLO 00000033f0808fc0 inflateInit_ + 0

0033f0a15130  003400000007 R_X86_64_JUMP_SLO 00000033f0806980 deflateInit2_ + 0

0033f0a15138  001800000007 R_X86_64_JUMP_SLO 0000000000000000 fclose + 0

0033f0a15140  002d00000007 R_X86_64_JUMP_SLO 00000033f08086c0 _tr_flush_block + 0

0033f0a15148  001900000007 R_X86_64_JUMP_SLO 0000000000000000 __sprintf_chk + 0

0033f0a15150  004500000007 R_X86_64_JUMP_SLO 00000033f08037f0 gzread + 0

0033f0a15158  001a00000007 R_X86_64_JUMP_SLO 0000000000000000 clearerr + 0

0033f0a15160  002c00000007 R_X86_64_JUMP_SLO 00000033f08021f0 adler32 + 0

0033f0a15168  001b00000007 R_X86_64_JUMP_SLO 0000000000000000 fwrite + 0

0033f0a15170  005700000007 R_X86_64_JUMP_SLO 00000033f080c870 inflate_table + 0

0033f0a15178  004900000007 R_X86_64_JUMP_SLO 00000033f08066a0 deflateParams + 0

0033f0a15180  003500000007 R_X86_64_JUMP_SLO 00000033f080cdd0 inflate_fast + 0

0033f0a15188  001c00000007 R_X86_64_JUMP_SLO 0000000000000000 fflush + 0

 

There are no unwind sections in this file.

 

Symbol table '.dynsym' contains 112 entries:

   Num:    Value          Size Type    Bind   Vis      Ndx Name

     0: 0000000000000000     0 NOTYPE  LOCAL  DEFAULT  UND

     1: 00000033f0801dd0     0 SECTION LOCAL  DEFAULT   10

     2: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND memset@GLIBC_2.2.5 (8)

     3: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND ftell@GLIBC_2.2.5 (8)

     4: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND __fprintf_chk@GLIBC_2.3.4 (9)

     5: 0000000000000000     0 NOTYPE  WEAK   DEFAULT  UND __gmon_start__

     6: 0000000000000000     0 NOTYPE  WEAK   DEFAULT  UND _Jv_RegisterClasses

     7: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fseek@GLIBC_2.2.5 (8)

     8: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND malloc@GLIBC_2.2.5 (8)

     9: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fopen@GLIBC_2.2.5 (8)

    10: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND __vsnprintf_chk@GLIBC_2.3.4 (9)

    11: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fputc@GLIBC_2.2.5 (8)

    12: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND free@GLIBC_2.2.5 (8)

    13: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND strlen@GLIBC_2.2.5 (8)

    14: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND ferror@GLIBC_2.2.5 (8)

    15: 0000000000000000     0 FUNC    WEAK   DEFAULT  UND __cxa_finalize@GLIBC_2.2.5 (8)

    16: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fdopen@GLIBC_2.2.5 (8)

    17: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND strerror@GLIBC_2.2.5 (8)

    18: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND strcat@GLIBC_2.2.5 (8)

    19: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND memcpy@GLIBC_2.2.5 (8)

    20: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fread@GLIBC_2.2.5 (8)

    21: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND __errno_location@GLIBC_2.2.5 (8)

    22: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND __stack_chk_fail@GLIBC_2.4 (10)

    23: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND strcpy@GLIBC_2.2.5 (8)

    24: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fclose@GLIBC_2.2.5 (8)

    25: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND __sprintf_chk@GLIBC_2.3.4 (9)

    26: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND clearerr@GLIBC_2.2.5 (8)

    27: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fwrite@GLIBC_2.2.5 (8)

    28: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND fflush@GLIBC_2.2.5 (8)

    29: 00000033f0802570   240 FUNC    GLOBAL DEFAULT   12 adler32_combine@@ZLIB_1.2.2

    30: 00000033f0807d10   955 FUNC    GLOBAL DEFAULT   12 _tr_align@@ZLIB_1.2.0

    31: 00000033f08042c0   126 FUNC    GLOBAL DEFAULT   12 gzdopen

    32: 00000033f08092a0    42 FUNC    GLOBAL DEFAULT   12 inflateSyncPoint

    33: 00000033f08030b0   206 FUNC    GLOBAL DEFAULT   12 gzclose

    34: 00000033f080b510    52 FUNC    GLOBAL DEFAULT   12 inflateBackEnd@@ZLIB_1.2.0

    35: 00000033f0808eb0   268 FUNC    GLOBAL DEFAULT   12 inflateInit2_

    36: 00000033f0802d10    42 FUNC    GLOBAL DEFAULT   12 gzclearerr@@ZLIB_1.2.0.2

    37: 00000033f08032c0    46 FUNC    GLOBAL DEFAULT   12 gzputc

    38: 00000033f08095e0   261 FUNC    GLOBAL DEFAULT   12 inflateSetDictionary

    39: 00000033f0802cf0    31 FUNC    GLOBAL DEFAULT   12 gzdirect@@ZLIB_1.2.2.3

    40: 00000033f0804350   235 FUNC    GLOBAL DEFAULT   12 uncompress

    41: 00000033f08033d0   284 FUNC    GLOBAL DEFAULT   12 gzprintf

    42: 00000033f0802a70   490 FUNC    GLOBAL DEFAULT   12 crc32_combine@@ZLIB_1.2.2

    43: 00000033f08080d0   165 FUNC    GLOBAL DEFAULT   12 _tr_tally@@ZLIB_1.2.0

    44: 00000033f08021f0   892 FUNC    GLOBAL DEFAULT   12 adler32

    45: 00000033f08086c0  1667 FUNC    GLOBAL DEFAULT   12 _tr_flush_block@@ZLIB_1.2.0

    46: 0000000000000000     0 OBJECT  GLOBAL DEFAULT  ABS ZLIB_1.2.0.2

    47: 00000033f0805b10  2954 FUNC    GLOBAL DEFAULT   12 deflate

    48: 00000033f0804470    55 FUNC    GLOBAL DEFAULT   12 deflatePrime@@ZLIB_1.2.0.8

    49: 00000033f0804340    10 FUNC    GLOBAL DEFAULT   12 gzopen

    50: 00000033f080d3a8     0 FUNC    GLOBAL DEFAULT   13 _fini@@ZLIB_1.2.0

    51: 00000033f08067b0    62 FUNC    GLOBAL DEFAULT   12 deflateBound@@ZLIB_1.2.0

    52: 00000033f0806980   741 FUNC    GLOBAL DEFAULT   12 deflateInit2_

    53: 00000033f080cdd0  1427 FUNC    GLOBAL DEFAULT   12 inflate_fast@@ZLIB_1.2.0

    54: 00000033f0802660    20 FUNC    GLOBAL DEFAULT   12 compressBound@@ZLIB_1.2.0

    55: 0000000000000000     0 OBJECT  GLOBAL DEFAULT  ABS ZLIB_1.2.0.8

    56: 00000033f0811400    53 OBJECT  GLOBAL DEFAULT   14 deflate_copyright@@ZLIB_1.2.0

    57: 00000033f0809020    45 FUNC    GLOBAL DEFAULT   12 inflateGetHeader@@ZLIB_1.2.2

    58: 00000033f0813340    47 OBJECT  GLOBAL DEFAULT   14 inflate_copyright@@ZLIB_1.2.0

    59: 00000033f0801dd0     0 FUNC    GLOBAL DEFAULT   10 _init@@ZLIB_1.2.0

    60: 00000033f0808d60     6 FUNC    GLOBAL DEFAULT   12 zlibCompileFlags@@ZLIB_1.2.0.2

    61: 00000033f0803280    55 FUNC    GLOBAL DEFAULT   12 gzputs

    62: 00000033f0811440   512 OBJECT  GLOBAL DEFAULT   14 _dist_code@@ZLIB_1.2.0

    63: 00000033f0a14da0    80 OBJECT  GLOBAL DEFAULT   20 z_errmsg@@ZLIB_1.2.0

    64: 00000033f080b410   241 FUNC    GLOBAL DEFAULT   12 inflateBackInit_@@ZLIB_1.2.0

    65: 0000000000000000     0 OBJECT  GLOBAL DEFAULT  ABS ZLIB_1.2.0

    66: 00000033f08092d0   398 FUNC    GLOBAL DEFAULT   12 inflateCopy@@ZLIB_1.2.0

    67: 0000000000000000     0 OBJECT  GLOBAL DEFAULT  ABS ZLIB_1.2.2

    68: 00000033f08044b0    53 FUNC    GLOBAL DEFAULT   12 deflateTune@@ZLIB_1.2.2.3

    69: 00000033f08037f0   794 FUNC    GLOBAL DEFAULT   12 gzread

    70: 00000033f08096f0  7450 FUNC    GLOBAL DEFAULT   12 inflate

    71: 00000033f0802680   224 FUNC    GLOBAL DEFAULT   12 compress2

    72: 00000033f0808db0   161 FUNC    GLOBAL DEFAULT   12 inflateReset

    73: 00000033f08066a0   266 FUNC    GLOBAL DEFAULT   12 deflateParams

    74: 00000033f0802760    11 FUNC    GLOBAL DEFAULT   12 compress

    75: 00000033f0803e20   174 FUNC    GLOBAL DEFAULT   12 gzsetparams

    76: 00000033f0803180   249 FUNC    GLOBAL DEFAULT   12 gzwrite

    77: 00000033f0808da0    10 FUNC    GLOBAL DEFAULT   12 zcalloc@@ZLIB_1.2.0

    78: 00000033f0803390    63 FUNC    GLOBAL DEFAULT   12 gzflush

    79: 00000033f0807b70   407 FUNC    GLOBAL DEFAULT   12 _tr_stored_block@@ZLIB_1.2.0

    80: 00000033f0802c60    87 FUNC    GLOBAL DEFAULT   12 gzungetc@@ZLIB_1.2.0.2

    81: 00000033f0808d50     8 FUNC    GLOBAL DEFAULT   12 zlibVersion

    82: 00000033f0808fc0    15 FUNC    GLOBAL DEFAULT   12 inflateInit_

    83: 00000033f0802780   744 FUNC    GLOBAL DEFAULT   12 crc32

    84: 00000033f0808d90     8 FUNC    GLOBAL DEFAULT   12 zcfree@@ZLIB_1.2.0

    85: 00000033f0809050   590 FUNC    GLOBAL DEFAULT   12 inflateSync

    86: 00000033f0804ea0   335 FUNC    GLOBAL DEFAULT   12 deflateSetDictionary

    87: 00000033f080c870  1368 FUNC    GLOBAL DEFAULT   12 inflate_table@@ZLIB_1.2.0

    88: 00000033f0802cc0    46 FUNC    GLOBAL DEFAULT   12 gzeof

    89: 00000033f0808fd0    78 FUNC    GLOBAL DEFAULT   12 inflateEnd

    90: 00000033f08044f0   263 FUNC    GLOBAL DEFAULT   12 deflateEnd

    91: 00000033f0803df0    41 FUNC    GLOBAL DEFAULT   12 gzgetc

    92: 00000033f0a15200     0 NOTYPE  GLOBAL DEFAULT  ABS _edata@@ZLIB_1.2.0

    93: 00000033f0804440    38 FUNC    GLOBAL DEFAULT   12 deflateSetHeader@@ZLIB_1.2.2

    94: 00000033f0811640   256 OBJECT  GLOBAL DEFAULT   14 _length_code@@ZLIB_1.2.0

    95: 0000000000000000     0 OBJECT  GLOBAL DEFAULT  ABS ZLIB_1.2.2.3

    96: 00000033f0803d40    12 FUNC    GLOBAL DEFAULT   12 gztell

    97: 00000033f08032f0   154 FUNC    GLOBAL DEFAULT   12 gzrewind

    98: 0000000000000000     0 OBJECT  GLOBAL DEFAULT  ABS ZLIB_1.2.2.4

    99: 00000033f0808d70    21 FUNC    GLOBAL DEFAULT   12 zError

   100: 00000033f0a15210     0 NOTYPE  GLOBAL DEFAULT  ABS _end@@ZLIB_1.2.0

   101: 00000033f08067f0   389 FUNC    GLOBAL DEFAULT   12 deflateReset

   102: 00000033f0804940   602 FUNC    GLOBAL DEFAULT   12 deflateCopy

   103: 00000033f080b550  4890 FUNC    GLOBAL DEFAULT   12 inflateBack@@ZLIB_1.2.0

   104: 00000033f0808e60    76 FUNC    GLOBAL DEFAULT   12 inflatePrime@@ZLIB_1.2.2.4

   105: 00000033f0806c70    41 FUNC    GLOBAL DEFAULT   12 deflateInit_

   106: 00000033f0803b10   560 FUNC    GLOBAL DEFAULT   12 gzseek

   107: 00000033f0802d40   307 FUNC    GLOBAL DEFAULT   12 gzerror

   108: 00000033f0a15200     0 NOTYPE  GLOBAL DEFAULT  ABS __bss_start@@ZLIB_1.2.0

   109: 00000033f0802770     8 FUNC    GLOBAL DEFAULT   12 get_crc_table

   110: 00000033f0806ca0   248 FUNC    GLOBAL DEFAULT   12 _tr_init@@ZLIB_1.2.0

   111: 00000033f0803d50   151 FUNC    GLOBAL DEFAULT   12 gzgets

 

Histogram for `.gnu.hash' bucket list length (total of 67 buckets):

Length  Number     % of total  Coverage

      0  17         ( 25.4%)

      1  23         ( 34.3%)     27.7%

      2  23         ( 34.3%)     83.1%

      3  3          (  4.5%)     94.0%

      4  0          (  0.0%)     94.0%

      5  1          (  1.5%)    100.0%

 

Version symbols section '.gnu.version' contains 112 entries:

Addr: 00000033f08013de  Offset: 0x0013de  Link: 3 (.dynsym)

  000:   0 (*local*)       0 (*local*)       8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)

  004:   9 (GLIBC_2.3.4)   0 (*local*)       0 (*local*)       8 (GLIBC_2.2.5)

  008:   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)   9 (GLIBC_2.3.4)   8 (GLIBC_2.2.5)

  00c:   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)

  010:   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)

  014:   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)   a (GLIBC_2.4)     8 (GLIBC_2.2.5)

  018:   8 (GLIBC_2.2.5)   9 (GLIBC_2.3.4)   8 (GLIBC_2.2.5)   8 (GLIBC_2.2.5)

  01c:   8 (GLIBC_2.2.5)   5 (ZLIB_1.2.2)    2 (ZLIB_1.2.0)    1 (*global*)

  020:   1 (*global*)      1 (*global*)      2 (ZLIB_1.2.0)    1 (*global*)

  024:   3 (ZLIB_1.2.0.2)   1 (*global*)      1 (*global*)      6 (ZLIB_1.2.2.3)

  028:   1 (*global*)      1 (*global*)      5 (ZLIB_1.2.2)    2 (ZLIB_1.2.0)

  02c:   1 (*global*)      2 (ZLIB_1.2.0)    3 (ZLIB_1.2.0.2)   1 (*global*)

  030:   4 (ZLIB_1.2.0.8)   1 (*global*)      2 (ZLIB_1.2.0)    2 (ZLIB_1.2.0)

  034:   1 (*global*)      2 (ZLIB_1.2.0)    2 (ZLIB_1.2.0)    4 (ZLIB_1.2.0.8)

  038:   2 (ZLIB_1.2.0)    5 (ZLIB_1.2.2)    2 (ZLIB_1.2.0)    2 (ZLIB_1.2.0)

  03c:   3 (ZLIB_1.2.0.2)   1 (*global*)      2 (ZLIB_1.2.0)    2 (ZLIB_1.2.0)

  040:   2 (ZLIB_1.2.0)    2 (ZLIB_1.2.0)    2 (ZLIB_1.2.0)    5 (ZLIB_1.2.2)

  044:   6 (ZLIB_1.2.2.3)   1 (*global*)      1 (*global*)      1 (*global*)

  048:   1 (*global*)      1 (*global*)      1 (*global*)      1 (*global*)

  04c:   1 (*global*)      2 (ZLIB_1.2.0)    1 (*global*)      2 (ZLIB_1.2.0)

  050:   3 (ZLIB_1.2.0.2)   1 (*global*)      1 (*global*)      1 (*global*)

  054:   2 (ZLIB_1.2.0)    1 (*global*)      1 (*global*)      2 (ZLIB_1.2.0)

  058:   1 (*global*)      1 (*global*)      1 (*global*)      1 (*global*)

  05c:   2 (ZLIB_1.2.0)    5 (ZLIB_1.2.2)    2 (ZLIB_1.2.0)    6 (ZLIB_1.2.2.3)

  060:   1 (*global*)      1 (*global*)      7 (ZLIB_1.2.2.4)   1 (*global*)

  064:   2 (ZLIB_1.2.0)    1 (*global*)      1 (*global*)      2 (ZLIB_1.2.0)

  068:   7 (ZLIB_1.2.2.4)   1 (*global*)      1 (*global*)      1 (*global*)

  06c:   2 (ZLIB_1.2.0)    1 (*global*)      2 (ZLIB_1.2.0)    1 (*global*)

 

Version definition section '.gnu.version_d' contains 7 entries:

  Addr: 0x00000033f08014c0  Offset: 0x0014c0  Link: 4 (.dynstr)

  000000: Rev: 1  Flags: BASE   Index: 1  Cnt: 1  Name: libz.so.1

  0x001c: Rev: 1  Flags: none  Index: 2  Cnt: 1  Name: ZLIB_1.2.0

  0x0038: Rev: 1  Flags: none  Index: 3  Cnt: 2  Name: ZLIB_1.2.0.2

  0x0054: Parent 1: ZLIB_1.2.0

  0x005c: Rev: 1  Flags: none  Index: 4  Cnt: 2  Name: ZLIB_1.2.0.8

  0x0078: Parent 1: ZLIB_1.2.0.2

  0x0080: Rev: 1  Flags: none  Index: 5  Cnt: 2  Name: ZLIB_1.2.2

  0x009c: Parent 1: ZLIB_1.2.0.8

  0x00a4: Rev: 1  Flags: none  Index: 6  Cnt: 2  Name: ZLIB_1.2.2.3

  0x00c0: Parent 1: ZLIB_1.2.2

  0x00c8: Rev: 1  Flags: none  Index: 7  Cnt: 2  Name: ZLIB_1.2.2.4

  0x00e4: Parent 1: ZLIB_1.2.2.3

 

Version needs section '.gnu.version_r' contains 1 entries:

Addr: 0x00000033f08015b0  Offset: 0x0015b0  Link: 4 (.dynstr)

  000000: Version: 1  File: libc.so.6  Cnt: 3

  0x0010:   Name: GLIBC_2.4  Flags: none  Version: 10

  0x0020:   Name: GLIBC_2.3.4  Flags: none  Version: 9

  0x0030:   Name: GLIBC_2.2.5  Flags: none  Version: 8

 

Notes at offset 0x000001c8 with length 0x00000024:

  Owner         Data size       Description

  GNU           0x00000014      NT_GNU_BUILD_ID (unique build ID bitstring)

 

Library list section '.gnu.liblist' contains 2 entries:

     Library              Time Stamp          Checksum   Version Flags

  0: libc.so.6            2016-02-23T09:02:06 0xe2c58dbe 0       0

  1: /lib64/ld-linux-x86- 2016-02-23T09:02:06 0xcb4dfea2 0       0

 

Here is what’s missing next to the blue text :

 

66: 00000000000101c0    13 FUNC    GLOBAL DEFAULT   12 gzopen64@@ZLIB_1.2.3.3

 

What do you guys think about this????

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

I  Bur. : 1-514-343-6111 poste 16568

 

 

 

-----Original Message-----
From: Peter Cock [mailto:[hidden email]]
Sent: May-26-16 3:32 AM
To: Fernandez Edgar <[hidden email]>; Nate Coraor <[hidden email]>
Cc: [hidden email]
Subject: Re: [galaxy-dev] not sure what I can do about this...

 

Sorry Edgar,

 

It looks like something else is causing this error (and my guess about different versions of Linux on Galaxy and the cluster was

wrong):

 

ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:

undefined symbol: gzopen64

 

It may be important how the pysam wheel was compiled, perhaps Nate may be able to comment (CC'd).

 

Peter

 

On Wed, May 25, 2016 at 12:40 PM, Fernandez Edgar <[hidden email]> wrote:

> Hello Peter,

> 

> For now, my new installation of galaxy v16.01 is on one test desktop running Oracle Linux 6.

> Before changing my production installation, I'm doing my due diligent.

> 

> Let me know what you think...

> 

> Edgar Fernandez


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Reply | Threaded
Open this post in threaded view
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Re: not sure what I can do about this...

fernandez Edgar
In reply to this post by Peter Cock
Hey guys,

I successfully fixed my problem.
Here's the solution if you would like to know:

1. download zlib-1.2.8.tar.gz
2. ./configure --prefix=/usr/local/zlib-1.2.8
3. make
4. make install
5. add the following in the file config/local_env.sh
        export LD_LIBRARY_PATH=/usr/local/zlib-1.2.8${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}



Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
I  Bur. : 1-514-343-6111 poste 16568


-----Original Message-----
From: Peter Cock [mailto:[hidden email]]
Sent: May-26-16 3:32 AM
To: Fernandez Edgar <[hidden email]>; Nate Coraor <[hidden email]>
Cc: [hidden email]
Subject: Re: [galaxy-dev] not sure what I can do about this...

Sorry Edgar,

It looks like something else is causing this error (and my guess about different versions of Linux on Galaxy and the cluster was
wrong):

ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
undefined symbol: gzopen64

It may be important how the pysam wheel was compiled, perhaps Nate may be able to comment (CC'd).

Peter

On Wed, May 25, 2016 at 12:40 PM, Fernandez Edgar <[hidden email]> wrote:
> Hello Peter,
>
> For now, my new installation of galaxy v16.01 is on one test desktop running Oracle Linux 6.
> Before changing my production installation, I'm doing my due diligent.
>
> Let me know what you think...
>
> Edgar Fernandez
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
12