Solved py27-numpy missing dependency

rhsbsd

rhsbsd

I never use ports. I don't even have a tree. User-land and kernel are in sync.
I can't seem to resolve this. I have completley rebuilt my installed packages with
pkg upgrade -f and still no good. What silly thing is going on here please?


Code: 
root@rhs:/home/Richard # uname -a
FreeBSD rhs.bsd 10.2-RELEASE-p7 FreeBSD 10.2-RELEASE-p7 #0: Mon Nov 2
14:19:39 UTC 2015 root@amd64-
builder.daemonology.net:/usr/obj/usr/src/sys/GENERIC amd64

root@rhs:/home/Richard # freebsd-version
10.2-RELEASE-p8

root@rhs:/home/Richard # pkg check -da
Checking all packages: 100%
py27-numpy has require a missing libraries: libopenblas.so

root@rhs:/home/Richard # find / -name "libopenblas.so"
/usr/local/lib/libopenblas.so

root@rhs:/etc pkg info openblas
openblas-0.2.14,1
Name : openblas
Version : 0.2.14,1
Installed on : Fri Nov 27 15:18:25 2015 EST
Origin : math/openblas
Architecture : freebsd:10:x86:64
Prefix : /usr/local
Categories : math
Licenses : BSD3CLAUSE
Maintainer : phd_kimberlite@yahoo.co.jp
WWW : https://github.com/xianyi/OpenBLAS
Comment : Optimized BLAS library based on GotoBLAS2
Options :
AVX : off
AVX2 : off
DYNAMIC_ARCH : on
INTERFACE64 : off
OPENMP : off
Shared Libs required:
libquadmath.so.0
libgfortran.so.3
Annotations :
repo_type : binary
repository : FreeBSD
Flat size : 145MiB
Description :
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
OpenBLAS is an open source project supported by
Lab of Parallel Software and Computational Science, ISCAS.
NOTE: If you want to specify your CPU microarchitecture manually,
please use TARGET_CPU_ARCH knob, e.g., "make TARGET_CPU_ARCH=NEHALEM".
This value is set TARGET build flag.
WWW: https://github.com/xianyi/OpenBLAS

root@rhs:/etc # pkg info py27-numpy
Name : py27-numpy
Version : 1.10.1,1
Installed on : Fri Nov 27 10:25:30 2015 EST
Origin : math/py-numpy
Architecture : freebsd:10:x86:64
Prefix : /usr/local
Categories : python math
Licenses : BSD3CLAUSE
Maintainer : python@FreeBSD.org
WWW : http://www.numpy.org/
Comment : The New Numeric Extension to Python
Options :
ATLAS : off
DOCS : on
NETLIB : on
OPENBLAS : off
SUITESPARSE : on
TESTS : off
Shared Libs required:
libblas.so.2
libpython2.7.so.1
libgcc_s.so.1
libquadmath.so.0
liblapack.so.4
libgfortran.so.3
libopenblas.so
Annotations :
repo_type : binary
repository : FreeBSD
Flat size : 20.8MiB
Description :
The fundamental package needed for scientific computing with Python is
called NumPy. This package contains:
* a powerful N-dimensional array object
* sophisticated (broadcasting) functions
* basic linear algebra functions
* basic Fourier transforms
* sophisticated random number capabilities
* tools for integrating Fortran code.
NumPy derives from the old Numeric code base and can be used as a
replacement for Numeric. It also adds the features introduced by numarray
and can also be used to replace numarray.
Note: Development for Numeric has ceased, and users should transisition to
NumPy as quickly as possible.
WWW: http://www.numpy.org/

#root@rhs:/usr/local/lib/libopenblas.so ll
lrwxr-xr-x  1 root  wheel  16 Nov 23 21:12 libopenblas.so@ -> libopenblas.so.0
And yes libopenblas.so.0 is there, 24.6meg.
At the moment it seems as if the link is not being followed?
 
I checked pkg updating but did not think to check the bug report as this just seemed like such a hard core failure. It looks as if they are having fun getting py27-numpy to build from ports and yes it appears that there are dependency issues. I guess the patch will show up in pkging sometime soon. I would like to mention that the pkging mechanism(s) have been working great for me. I follow current, not the quarterly pkg upgrade set up as default. That may be why this happened as well. Thanks again chrbr.
 
A commit has been submitted by port maintainer Olivier Duchateau for math/py-numpy. See comment #3 as reported in PR 203840. I guess that since math/py-numpy is listed as an 'Origin' in pkg info py27-numpy that this change will take effect when the commit is actually in head and I re-build the pkg locally?
 
For my system updating the ports tree and updating math/py-numpy by portmaster py27-numpy was successful. Before that I have had modified the Makefile according to the problem report. I guess that the update should appear in the pkg system after some days. Others will know that better than myself.
 
Thanks chrbr . As others are purists in there own fashion I too have become a purist; i.e. purely using packages now for 1yr. It has worked flawlessly save for apparent dependency issues with package py27-numpy. Package py27-numpy has just recently been bumped due to port revision in origin math/py-numpy So now after recursively installing py27-numpy I have the following:
Code: 
# pkg info --dependencies py27-numpy
py27-numpy-1.10.2,1:
  python27-2.7.11
  py27-setuptools27-19.2
  gcc-4.8.5_2
  suitesparse-4.0.2_4
  blas-3.5.0_3
  lapack-3.5.0
  cblas-1.0_4
# pkg check -d
Checking all packages: 100%
py27-numpy has require a missing libraries: libopenblas.so
So as you can see pkg check -d either thinks that
libopenblas.so is still actually a dependency of package py27-numpy or possibly pkg check -d is failing to properly report, or just please tell me what to do! The dependencies as listed by pkg info --dependencies py27-numpy do exist presently as reported by pkg info. In addition I cannot find libopenblas.so listed as a provided shared library. I would of preffered to report this as solved.
 
Dear rhsbsd,
please run make config in /usr/ports/math/py-numpy and check the option Netlib. Then re-compile the port for example by portmaster py27-numpy. I think this should help.
 
chrbr what you propose will work as this is what I myself have done on builds in the past but, that is precisely why I must wait for the packaging mechanism to correct itself. In a perfect world a generic kernel and using only packaging should not have this problem. So something needs a little help. I will wait! Just to clarify "I will not be drawn into the unknown."
 
Did a pkg upgrade today and it included the following:
Code: 
New packages to be INSTALLED:
  ruby21: 2.1.8,1
  ruby22-bdb: 0.6.6_4

Installed packages to be UPGRADED:
  pkg: 1.7.0 -> 1.7.2
  xapian-core: 1.2.22,1 -> 1.2.23,1
  wireshark: 2.0.2 -> 2.0.2_1
  webp: 0.4.4_1 -> 0.5.0
  webkit2-gtk3: 2.8.5 -> 2.8.5_2
  webkit-gtk2: 2.4.9_1 -> 2.4.9_2
  vlc-qt4: 2.2.1_7,4 -> 2.2.1_8,4
  ruby: 2.1.8,1 -> 2.2.4,1
  rar: 5.2.1,3 -> 5.3.0,3
  py27-pillow: 3.1.1 -> 3.1.1_1
  postgresql93-client: 9.3.11 -> 9.3.12
  perl5: 5.20.3_8 -> 5.20.3_9
  pcre: 8.38 -> 8.38_1
  p5-Params-Validate: 1.22 -> 1.23
  p5-DateTime-TimeZone: 1.96 -> 1.97
  p5-Archive-Zip: 1.56 -> 1.57
  openjdk8: 8.72.15 -> 8.77.3
  openblas: 0.2.15,1 -> 0.2.15_1,1
  nmap: 7.11 -> 7.12
  llvm37: 3.7.1 -> 3.7.1_1
  libvncserver: 0.9.9_11 -> 0.9.9_12
  libgcrypt: 1.6.5 -> 1.6.5_1
  libedit: 3.1.20150325_1 -> 3.1.20150325_2
  kde-runtime: 4.14.3_1 -> 4.14.3_2
  gutenprint-cups: 5.2.10_2 -> 5.2.10_3
  gtk3: 3.18.8_1 -> 3.18.8_3
  gtk2: 2.24.29_1 -> 2.24.29_2
  graphite2: 1.3.7 -> 1.3.8
  gnutls: 3.3.17.1_3 -> 3.4.10
  gnupg: 2.1.11_1 -> 2.1.11_2
  glib-networking: 2.46.1 -> 2.46.1_1
  gimp-app: 2.8.16_1,1 -> 2.8.16_2,1
  ghostscript9-agpl-base: 9.16_4 -> 9.16_5
  ffmpeg: 2.8.6,1 -> 2.8.6_2,1
  emacs24: 24.5_2,3 -> 24.5_3,3
  curl: 7.48.0 -> 7.48.0_1
  cups-filters: 1.8.2_4 -> 1.8.3
  alsa-plugins: 1.1.0_1 -> 1.1.1
  alsa-lib: 1.1.0 -> 1.1.1
  ImageMagick: 6.9.3.7_1,1 -> 6.9.3.7_2,1

Installed packages to be REINSTALLED:
  py27-numpy-1.11.0,1 (needed shared library changed)
  portupgrade-2.4.14,2 (direct dependency changed: ruby22-bdb)
  json-glib-1.1.2 (option added: GIR)

The process will require 41 MiB more space.
368 MiB to be downloaded.
This is now resolved.
Code: 
# pkg check -d -a
Checking all packages: 100%
 
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