Re: [galaxy-dev] atlas version 3.10.2 installation error

19 Apr 2017

      Oh right - I've just been updating ncbi_blast_plus this morning
to transition to BLAST+ 2.5.0 via either bioconda or the older
legacy Tool Shed.

I can try to update blast_rbh next, which may solve this by
letting you use bioconda.

Peter

On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.bernt@ufz.de> wrote:
...
Dear Marius,
thanks again for the help. I'm trying to install blast_rbh (owner is
peterjc). The dependencies look as follows:
blast_rbh
- biopython
  - package_biopython_1_64
    - package_numpy_1_8
      - package_atlas_3_10
- blast
    - package_blast_plus_2_2_31
      - blast+
With unchecked "When available, install Tool Shed managed tool
dependencies?" I get all as "Installed, missing tool dependencies".
Blast_rbh is not working since blast+ is not installed. Even if I install
blast+ manually (in galaxy) its not working (makeblastdb is missing).
When I leave "When available, install Tool Shed managed tool dependencies?"
I see blast_rbh, package_blast_plus package_biopython as installed and the
others as Installed, missing tool dependencies.
Here blast_rbh is working.
What would be your suggestion? Live with the latter and file an issue at the
tools repository (difficult to say which causes the problem(s))?
I get similar behavior if I try to install from the test toolshed.
(Only a different error from atlas: /bin/sh: line 3:
/host/static_full_blas_lapack.diff: No such file or directory).
But, actually I'm trying to automatize tool installation using the ansible
role ansible-galaxy-tools
(https://github.com/galaxyproject/ansible-galaxy-tools). With this method I
get the latter behavior. The role uses uses ephemeris==0.4.0 to install
tools. There I have seen three global variables that (I guess) control the
installation of dependencies.
INSTALL_TOOL_DEPENDENCIES = False
INSTALL_REPOSITORY_DEPENDENCIES = True
INSTALL_RESOLVER_DEPENDENCIES = True
I guess I could control the behavior with the latter two variables.
Best,
Matthias
On 18.04.2017 19:24, Marius van den Beek wrote:
...
Hi Matthias,
it's me again!
What tool are you trying to install?
My -perhaps- unhelpful suggestion is to not install anything that starts
with
package_* (also called tool shed packages), those should be exclusively
installed when you absolutely need
to install an old tool that can only function with packages.
We've switched to conda nowadays, which is much easier to install and to
maintain.
In fact the IUC has ported all their latest tools to conda, and
similarly most devteam
tools that are still in active use have also been ported to use Conda
dependencies.
If you look at this
document
https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/,
there is a part where you confirm dependencies. If you click on show
detail, and you unselect
When available, install Tool Shed managed tool dependencies?
Galaxy will not try to install these old packages. There are some tools
which come both with
old toolshed dependencies and that have Conda available. You may be
lucky and find that
the tool you are trying to install has Conda dependencies available.
There is a lot more background on the Toolshed and Conda in this
document here:
https://docs.galaxyproject.org/en/master/admin/conda_faq.html
Best,
Marius
On 18 April 2017 at 19:03, Matthias Bernt <m.bernt@ufz.de
<mailto:m.bernt@ufz.de>> wrote:
Dear list,
again me :( stumbling from problem to problem ...
I got compilation errors when installing
package_atlas_3_10 Revision: 98c017ec230d
I tried with gcc 4x and 6x without success. Do I need the intel C
    compiler for this tool?
If I got earlier posts
    (http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html
<http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>)
correct a precompiled version should be used anyway?
I'm running galaxy on CentOS 6.8 (64bit) (running in a VirtualBox).
Best,
    Matthias
Here is the output (which I guess is verbose output from configure):
/tmp/cctyMGAH.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    probe_OS.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    probe_asm.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2>
    /dev/null | fgrep SUCCESS)
ierr=256 in command='make IRun_GAS_x8632 args="-v 2"
    MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'!
OUTPUT:
    =======
    system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2>
    /dev/null | fgrep SUCCESS)
    probe_vec.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
ierr=256 in command='make IRun_VSX MYFLAGS='-DATL_OS_Linux
    -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
OUTPUT:
    =======
ierr=256 in command='make IRun_AltiVec MYFLAGS='-DATL_OS_Linux
    -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
OUTPUT:
    =======
ierr=256 in command='make IRun_AVXFMA4 MYFLAGS='-DATL_OS_Linux
    -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
OUTPUT:
    =======
ierr=256 in command='make IRun_3DNow MYFLAGS='-DATL_OS_Linux
    -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
OUTPUT:
    =======
ierr=256 in command='make IRun_NEON MYFLAGS='-DATL_OS_Linux
    -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
OUTPUT:
    =======
    probe_arch.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    /tmp/cc8hbxc1.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    ERROR: enum fam=3, chip=2, model=79, mach=0
    make[3]: *** [atlas_run] Error 44
    make[2]: *** [IRunArchInfo_x86] Error 2
    /tmp/ccafA8Bi.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    ERROR: enum fam=3, chip=2, model=79, mach=0
    make[3]: *** [atlas_run] Error 44
    make[2]: *** [IRunArchInfo_x86] Error 2
    ERROR: enum fam=3, chip=2, model=79, mach=0
    make[3]: *** [atlas_run] Error 44
    make[2]: *** [IRunArchInfo_x86] Error 2
    cmnd='make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77
    0 -V 488  -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk
    '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC'
    -b 64"'
    /tmp/cc8W8Itx.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
    probe_comp.o: In function `ATL_tmpnam':
/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
    warning: the use of `tmpnam' is dangerous, better use `mkstemp'
ierr=256 in command='find
    /gpfs1/data/galaxy_server/galaxy-dev/.venv/bin
    /usr/local/gcc/6.2.0-1/bin
    /global/apps/bioinf/galaxy/bin/Python-2.7.13/bin
    /usr/local/sqlite/3.15.1-1/bin
    /global/apps/bioinf/galaxy/bin/postgresql-9.6.2/bin
    /usr/local/git/2.10.1-1/bin /usr/local/pcre/8.38-1/bin
    /usr/local/ncurses/5.9-1/bin /usr/local/bzip2/1.0.6-3/bin
    /usr/local/expat/2.1.1-1/bin /usr/local/curl/7.41.0-1/bin
    /usr/local/openssl/1.0.2-1/usr/bin
    /usr/local/uge/8.4.4-1/bin/lx-amd64 /usr/local/bin /bin /usr/bin
    /usr/local/sbin /usr/sbin /sbin /home/songalax/bin -maxdepth 1 -name
    '*gcc*' -exec ./xisgcc '{}' \;'!
OUTPUT:
    =======
    cmnd=make IRunCComp CC='/usr/local/gcc/6.2.0-1/bin/gcc'
    CCFLAGS='-O'  | fgrep SUCCESS
       /usr/local/gcc/6.2.0-1/bin/gcc -O : SUCCESS!
    cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O'  | fgrep SUCCESS
       /usr/bin/gcc -O : SUCCESS!
    sh: -c: line 0: unexpected EOF while looking for matching ``'
    sh: -c: line 1: syntax error: unexpected end of file
ierr=256 in command='find $HOME/local -name '*gcc*' -exec ./xisgcc
    '{}' \;'!
OUTPUT:
    =======
    cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O'  | fgrep SUCCESS
       /usr/bin/gcc -O : SUCCESS!
    sh: -c: line 0: unexpected EOF while looking for matching ``'
    sh: -c: line 1: syntax error: unexpected end of file
ierr=256 in command='find /usr/local /bin /sbin /usr/bin /usr/sbin
    /opt/bin /opt/sbin -name '*gcc*' -exec ./xisgcc '{}' \;'!
OUTPUT:
    =======
    cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O'  | fgrep SUCCESS
       /usr/bin/gcc -O : SUCCESS!
    sh: -c: line 0: unexpected EOF while looking for matching ``'
    sh: -c: line 1: syntax error: unexpected end of file
    sh: -c: line 0: unexpected EOF while looking for matching ``'
    sh: -c: line 1: syntax error: unexpected end of file
Compiler nodes: Fresh Read
      0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77'
         '-O'
      1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77'
         '-O'
      2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran'
         '-O'
      3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc'
         '-O -fomit-frame-pointer'
      4. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
         '-mcpu=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -O'
      5. priority=1000, comps,OS,arch[0]=(20,1,0), comp='gcc'
         '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3
    -mfloat-abi=softfp -fno-schedule-insns2'
      6. priority=1000, comps,OS,arch[0]=(75,1,0), comp='gcc'
         '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3
    -mfloat-abi=softfp -fno-expensive-optimizations'
      7. priority=1000, comps,OS,arch[0]=(32,1,0), comp='gcc'
         '-mcpu=cortex-a8 -O1 -mfpu=vfpv3 -mfloat-abi=softfp '
      8. priority=0, comps,OS,arch[0]=(63,768,1075838976), comp='icl'
         '-QxN -O3 -Qprec -fp:extended -fp:except -nologo -Oy'
      9. priority=0, comps,OS,arch[0]=(128,768,1), comp='ifort'
         '-O2 -fltconsistency -nologo'
     10. priority=0, comps,OS,arch[0]=(63,768,1), comp='cl'
         '-Oy -Ox -arch:SSE2 -nologo'
     11. priority=4, comps,OS,arch[0]=(63,768,1048576), comp='cl'
         '-Oy -Ox -arch:SSE -nologo'
     12. priority=4, comps,OS,arch[0]=(63,768,983040), comp='cl'
         '-Oy -Ox'
     13. priority=500, comps,OS,arch[0]=(127,1,3584), comp='gcc'
         '-O3 -funroll-loops'
     14. priority=500, comps,OS,arch[0]=(128,1,3584), comp='gfortran'
         '-O3 -funroll-loops'
     15. priority=600, comps,OS,arch[0]=(128,1,2048), comp='gfortran'
         '-march=z9-109 -O3 -funroll-loops'
     16. priority=600, comps,OS,arch[0]=(127,1,2048), comp='gcc'
         '-march=z9-109 -O3 -funroll-loops'
     17. priority=800, comps,OS,arch[0]=(128,1,2048), comp='gfortran'
         '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays'
     18. priority=800, comps,OS,arch[0]=(127,1,2048), comp='gcc'
         '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays'
     19. priority=1000, comps,OS,arch[0]=(127,1,2048), comp='gcc'
         '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays'
     20. priority=1000, comps,OS,arch[0]=(128,1,2048), comp='gfortran'
         '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays'
     21. priority=600, comps,OS,arch[0]=(127,1,1024), comp='gcc'
         '-march=z9-109 -O3 -funroll-loops -fno-prefetch-loop-arrays'
     22. priority=600, comps,OS,arch[0]=(128,1,1024), comp='gfortran'
         '-march=z9-109 -O3 -funroll-loops'
     23. priority=1000, comps,OS,arch[0]=(127,1,1024), comp='gcc'
         '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays'
     24. priority=1000, comps,OS,arch[0]=(127,1,512), comp='gcc'
         '-march=z9-109 -O3 -funroll-loops'
     25. priority=1010, comps,OS,arch[0]=(128,1,4), comp='xlf'
         '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt'
     26. priority=1010, comps,OS,arch[0]=(127,1,4), comp='gcc'
         '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns
    -fno-rerun-loop-opt'
     27. priority=1010, comps,OS,arch[0]=(128,1,8), comp='xlf'
         '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt'
     28. priority=1010, comps,OS,arch[0]=(128,1,128), comp='xlf'
         '-qtune=pwr7 -qarch=pwr7 -O3 -qmaxmem=-1 -qfloat=hsflt'
     29. priority=1010, comps,OS,arch[0]=(128,1,8), comp='gfortran'
         '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns
    -fno-rerun-loop-opt'
     30. priority=1010, comps,OS,arch[0]=(128,1,64), comp='gfortran'
         '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns
    -fschedule-insns2 -minsert-sched-nops=2'
     31. priority=1010, comps,OS,arch[0]=(127,1,8), comp='gcc'
         '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns
    -fno-rerun-loop-opt'
     32. priority=1010, comps,OS,arch[0]=(127,1,64), comp='gcc'
         '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns
    -fschedule-insns2 -minsert-sched-nops=2'
     33. priority=1010, comps,OS,arch[0]=(128,1,128), comp='gfortran'
         '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave
    -funroll-all-loops'
     34. priority=1010, comps,OS,arch[0]=(127,1,128), comp='gcc'
         '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave
    -funroll-all-loops'
     35. priority=1000, comps,OS,arch[0]=(8,1,32), comp='gcc'
         '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2
    -mvrsave'
     36. priority=1000, comps,OS,arch[0]=(117,1,32), comp='gcc'
         '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2'
     37. priority=1000, comps,OS,arch[0]=(2,1,32), comp='gcc'
         '-Os -mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970
    -mvrsave -fno-schedule-insns2 -fno-schedule-insns'
     38. priority=1000, comps,OS,arch[0]=(121,1,16), comp='gcc'
         '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400
    -fno-schedule-insns -fschedule-insns2'
     39. priority=1000, comps,OS,arch[0]=(2,1,16), comp='gcc'
         '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400'
     40. priority=1000, comps,OS,arch[0]=(4,1,16), comp='gcc'
         '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400'
     41. priority=1, comps,OS,arch[0]=(33,1,0), comp='pathcc'
         '-march=auto -O2 -OPT:Olimit=15000 -LNO:blocking=OFF'
     42. priority=1, comps,OS,arch[0]=(6,1,0), comp='pathcc'
         '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed
    -march=auto -LNO:opt=0 -LNO:full_unroll_outer=OFF -LNO:fusion=0
    -LNO:prefetch=2'
     43. priority=1, comps,OS,arch[0]=(24,1,0), comp='pathcc'
         '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed
    -march=auto'
     44. priority=1000, comps,OS,arch[0]=(128,1,0), comp='pathf95'
         '-march=auto -O2'
     45. priority=500, comps,OS,arch[0]=(127,1,0), comp='gcc'
         '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns
    -fschedule-insns2 -fno-peephole -fno-peephole2'
     46. priority=1000, comps,OS,arch[0]=(128,32,0), comp='f77'
         '-O2'
     47. priority=1000, comps,OS,arch[0]=(97,32,0), comp='cc'
         '-O2 -OPT:Olimit=15000 -LNO:blocking=OFF'
     48. priority=1000, comps,OS,arch[0]=(30,32,0), comp='cc'
         '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed'
     49. priority=1010, comps,OS,arch[0]=(128,1,0), comp='gfortran'
         '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
     50. priority=1000, comps,OS,arch[0]=(30,1,0), comp='gcc'
         '-fomit-frame-pointer -O2'
     51. priority=1010, comps,OS,arch[0]=(30,1,0), comp='gcc'
         '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
     52. priority=10, comps,OS,arch[0]=(128,1,0), comp='g77'
         '-O -mcpu=ultrasparc3 -mtune=ultrasparc3'
     53. priority=100, comps,OS,arch[0]=(128,1,0), comp='gfortran'
         '-O -mcpu=ultrasparc3 -mtune=ultrasparc3'
     54. priority=1000, comps,OS,arch[0]=(128,1,0), comp='f77'
         '-dalign -native -xO5'
     55. priority=1000, comps,OS,arch[0]=(96,1,0), comp='gcc'
         '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O'
     56. priority=1000, comps,OS,arch[0]=(29,1,0), comp='gcc'
         '-O3 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fno-schedule-insns2
    -fschedule-insns'
     57. priority=1000, comps,OS,arch[0]=(2,1,0), comp='gcc'
         '-O1 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fschedule-insns
    -fmodulo-sched'
     58. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
         '-mcpu=niagara2 -mtune=niagara2 -Os'
     59. priority=1000, comps,OS,arch[0]=(127,1,0), comp='gcc'
         '-mcpu=niagara2 -mtune=niagara2 -Os'
     60. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -mfma4 -O2
    -fno-tree-loop-optimize'
     61. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
         '-Os -fomit-frame-pointer'
     62. priority=1005, comps,OS,arch[0]=(95,896,0), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     63. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     64. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     65. priority=1000, comps,OS,arch[0]=(95,1,12582912), comp='gcc'
         '-fomit-frame-pointer -O3 -mfpmath=387'
     66. priority=1005, comps,OS,arch[0]=(31,896,12582912), comp='gcc-4'
         '-fomit-frame-pointer -O3 -mfpmath=387'
     67. priority=1000, comps,OS,arch[0]=(95,1,-1071906816), comp='gcc'
         '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
     68. priority=1005, comps,OS,arch[0]=(31,896,1835008), comp='gcc-4'
         '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
     69. priority=1000, comps,OS,arch[0]=(128,1,1835008), comp='gfortran'
         '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
     70. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
         '-fomit-frame-pointer -mfpmath=387 -O2'
     71. priority=1005, comps,OS,arch[0]=(31,896,0), comp='gcc-4'
         '-fomit-frame-pointer -mfpmath=387 -O2'
     72. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
         '-fomit-frame-pointer -mfpmath=387 -O2'
     73. priority=1000, comps,OS,arch[0]=(25,1,-1073741824), comp='gcc-4'
         '-O2 -fomit-frame-pointer -mfpmath=sse'
     74. priority=1005, comps,OS,arch[0]=(6,896,-1073741824), comp='gcc-4'
         '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns
    -fno-optimize-register-move'
     75. priority=1000, comps,OS,arch[0]=(6,1,-1073741824), comp='gcc'
         '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns
    -fno-optimize-register-move'
     76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648), comp='gcc'
         '-O2 -fomit-frame-pointer -mfpmath=sse'
     77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824),
    comp='gfortran'
         '-O2 -fomit-frame-pointer -mfpmath=sse'
     78. priority=1000, comps,OS,arch[0]=(128,1,32768), comp='gfortran'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     80. priority=1000, comps,OS,arch[0]=(128,1,16384), comp='gfortran'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     82. priority=1000, comps,OS,arch[0]=(128,1,8192), comp='gfortran'
         '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
     83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc'
         '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
     85. priority=1000, comps,OS,arch[0]=(128,1,12288), comp='gfortran'
         '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
     86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc'
         '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
     87. priority=1000, comps,OS,arch[0]=(65,1,536870912), comp='gcc'
         '-O'
     88. priority=1000, comps,OS,arch[0]=(30,1,536870912), comp='gcc'
         '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch'
     89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     90. priority=1005, comps,OS,arch[0]=(31,896,33554432), comp='gcc-4'
         '-fomit-frame-pointer -mfpmath=sse -O2'
     91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
     92. priority=1005, comps,OS,arch[0]=(95,896,67108864), comp='gcc-4'
         '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
     93. priority=50, comps,OS,arch[0]=(57,1,134217728), comp='clang'
         '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses'
     94. priority=1000, comps,OS,arch[0]=(127,1,134217728), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
     95. priority=1005, comps,OS,arch[0]=(31,896,134217728), comp='gcc-4'
         '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
     96. priority=1000, comps,OS,arch[0]=(127,1,268435456), comp='gcc'
         '-fomit-frame-pointer -mfpmath=sse -O2'
Compiler nodes: Targeted
      0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77'
         '-O'
      1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77'
         '-O'
      2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran'
         '-O'
      3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc'
         '-O -fomit-frame-pointer'
Compiler nodes: Sorted
      0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77'
         '-O'
      1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77'
         '-O'
      2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc'
         '-O -fomit-frame-pointer'
      3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran'
         '-O'
cc1: error: unrecognized command line option "-mavx2"
    make[2]: *** [IRunCComp] Error 1
ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O
    -fomit-frame-pointer -mavx2 -mfma -fPIC -m64'  | fgrep SUCCESS'!
OUTPUT:
    =======
    cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O
    -fomit-frame-pointer -mavx2 -mfma -fPIC -m64'  | fgrep SUCCESS
       /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 :
    FAILURE!
Unable to find usable compiler for ICC; abortingMake sure compilers
    are in your path, and specify good compilers to configure
    (see INSTALL.txt or 'configure --help' for details)make[1]: ***
    [atlas_run] Error 1
    make: *** [IRun_comp] Error 2
    ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt -O 1
    -A 39 -Si nof77 0 -V 488  -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm
    '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC'
    -Fa if '-fPIC' -b 64"'
    Make.top:1: Make.inc: No such file or directory
    Make.top:329: warning: overriding commands for target `/AtlasTest'
    Make.top:80: warning: ignoring old commands for target `/AtlasTest'
    make[1]: *** No rule to make target `Make.inc'.  Stop.
    make: *** [startup] Error 2
    mv: cannot stat `lib/Makefile': No such file or directory
    ../configure: line 450: lib/Makefile: No such file or directory
    ../configure: line 451: lib/Makefile: No such file or directory
    ../configure: line 452: lib/Makefile: No such file or directory
    ../configure: line 453: lib/Makefile: No such file or directory
    ../configure: line 509: lib/Makefile: No such file or directory
    Make.top:1: Make.inc: No such file or directory
    Make.top:329: warning: overriding commands for target `/AtlasTest'
    Make.top:80: warning: ignoring old commands for target `/AtlasTest'
    make[1]: *** No rule to make target `Make.inc'.  Stop.
    make: *** [build] Error 2
    --
-------------------------------------------
    Matthias Bernt
    Bioinformatics Service
    Molekulare Systembiologie (MOLSYB)
    Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
    Helmholtz Centre for Environmental Research GmbH - UFZ
    Permoserstraße 15, 04318 Leipzig, Germany
    Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>,
    m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de>
Sitz der Gesellschaft/Registered Office: Leipzig
    Registergericht/Registration Office: Amtsgericht Leipzig
    Handelsregister Nr./Trade Register Nr.: B 4703
    Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
    MinDirig Wilfried Kraus
    Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
    Prof. Dr. Dr. h.c. Georg Teutsch
    Administrative Geschäftsführerin/ Administrative Managing Director:
    Prof. Dr. Heike Graßmann
    -------------------------------------------
___________________________________________________________
    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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at:
      http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
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/

Re: [galaxy-dev] atlas version 3.10.2 installation error

Peter Cock