Opened 4 years ago

Last modified 3 years ago

#52686 assigned defect

gmt4 @4.5.14_2 : error building gmt4 during install

Reported by: NestorCerpa Owned by: tenomoto (Takeshi Enomoto)
Priority: Normal Milestone:
Component: ports Version: 2.3.4
Keywords: Cc:
Port: gmt4

Description

I tried to install gmt4 on my MacBook Air OSX Yosemite 10.10.5 but I have a problem.

During the first build it says : " Error: org.macports.build for port gmt4 returned: command execution failed"

Attachments (1)

main.log (65.9 KB) - added by NestorCerpa 4 years ago.
Log file failed installation gmt4

Download all attachments as: .zip

Change History (5)

Changed 4 years ago by NestorCerpa

Attachment: main.log added

Log file failed installation gmt4

comment:1 in reply to:  description Changed 4 years ago by ken-cunningham-webuse

error is

ld: library not found for -lhdf5_hl

but I see you have "hdf5-18 1.8.17_0" installed.

port search hdf5 shows

hdf5 @1.10.0-patch1 (science)
    HDF5 general purpose library and file format for storing scientific data

hdf5-18 @1.8.17 (science)
    HDF5 general purpose library and file format for storing scientific data

that's a bit odd. I know nothing about this port, but a missing library is a missing library. Do you have the library? locate hdf5_hl or perhaps ls -la /opt/local/lib/libhdf*

If not, perhaps you need that other hdf5 install, or perhaps you don't have the +hl variant installed (which it seems to be looking for)? port -v installed | grep hdf5 will show you what you have already.

If you do have the library, but it won't use it, that's another entire matter.

Hope this helps get you started.

Last edited 4 years ago by ken-cunningham-webuse (previous) (diff)

comment:2 Changed 4 years ago by ryandesign (Ryan Schmidt)

Cc: takeshi@… added
Owner: changed from macports-tickets@… to florian@…
Status: newassigned

comment:3 Changed 3 years ago by anowacki (Andy Nowacki)

This occurs because the hdf5-18 port installs into /opt/local/lib/hdf5-18, but this directory is not added to the linker options by the port file for gmt4. hdf5-18 is a dependency of gmt via netcdf with the +netcdf4 variant.

I noticed this issue when upgrading to Sierra and installed in the order gmt4, gmt5, which did not install hdf5 first. GMT seems to link to hdf5 fine and I haven't been able to find any problems with this.

I guess the correct fix is to add linker commands to point to /opt/local/lib/hdf5-18, though I could only speculate why netcdf +netcdf4 necessarily has to use hdf5-18. A current workaround is to just install hdf5 first.

comment:4 Changed 3 years ago by raimue (Rainer Müller)

Cc: tenomoto removed
Owner: changed from florian@… to tenomoto

Port abandoned, #54396.

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