Re: [julia-users] Unable to add HDF5
Strange. That commit is present in the repository: see https://github.com/timholy/HDF5.jl/commits/master Anyone else having the same problem? I just did this and it went off without a hitch (julia-old is my installation of the 0.3 release): $ mkdir /tmp/packages $ JULIA_PKGDIR=/tmp/packages julia-old _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_)| Documentation: http://docs.julialang.org _ _ _| |_ __ _ | Type help() for help. | | | | | | |/ _` | | | | |_| | | | (_| | | Version 0.3.7-pre+1 (2015-02-17 22:12 UTC) _/ |\__'_|_|_|\__'_| | Commit d15f183* (153 days old release-0.3) |__/ | x86_64-linux-gnu julia Pkg.init() INFO: Initializing package repository /tmp/packages/v0.3 INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl julia Pkg.add(HDF5) INFO: Cloning cache of BinDeps from git://github.com/JuliaLang/BinDeps.jl.git INFO: Cloning cache of Blosc from git://github.com/stevengj/Blosc.jl.git INFO: Cloning cache of Compat from git://github.com/JuliaLang/Compat.jl.git INFO: Cloning cache of HDF5 from git://github.com/timholy/HDF5.jl.git INFO: Cloning cache of SHA from git://github.com/staticfloat/SHA.jl.git INFO: Cloning cache of URIParser from git://github.com/JuliaWeb/URIParser.jl.git INFO: Installing BinDeps v0.3.14 INFO: Installing Blosc v0.1.2 INFO: Installing Compat v0.4.9 INFO: Installing HDF5 v0.5.0 INFO: Installing SHA v0.0.4 INFO: Installing URIParser v0.0.5 INFO: Building Blosc % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 1210 1210 0553 0 --:--:-- --:--:-- --:--:-- 555 0 00 233k0 0 221k 0 --:--:-- 0:00:01 --:--:-- 427k Compiling libblosc... CC blosc.c CC blosclz.c CC shuffle.c LINK libblosc INFO: Building HDF5 INFO: Package database updated julia which went like a charm. Maybe try Pkg.update()? --Tim On Monday, July 20, 2015 10:36:25 PM Roger Herikstad wrote: Hi, For some reason I am unable to add HDF5. Not sure if this is related to the recent change splitting JLD off into its own package. This is the error I got ulia Pkg.add(HDF5) INFO: Updating cache of HDF5... ERROR: Missing package versions (possible metadata misconfiguration): HDF5 v(nothing,v0.5.0) [883165af1cef09980a3d9b1718477579d629754c[1:10]] in wait at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib (repeats 2 times) in wait at task.jl:48 in sync_end at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib in add at pkg/entry.jl:319 in add at pkg/entry.jl:71 in anonymous at pkg/dir.jl:28 in cd at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib in __cd#229__ at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib in add at pkg.jl:20 This is my versioninfo: julia versioninfo() Julia Version 0.3.10 Commit c8ceeef* (2015-06-24 13:54 UTC) Platform Info: System: Darwin (x86_64-apple-darwin13.4.0) CPU: Intel(R) Xeon(R) CPU X5472 @ 3.00GHz WORD_SIZE: 64 BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn) LAPACK: libopenblas LIBM: libopenlibm LLVM: libLLVM-3.3 I appreciate any advice on what the problem might be. Thanks!
Re: [julia-users] Unable to add HDF5
Hm, just tried Pkg.update() on 0.4.0-dev+5955 and I got the new version of HDF5 without any problems, so there's probably something wonky going on with Pkg on my 0.3.10. Is there anything I can do to try and reset Pkg, short of nuking my whole ~/.julia/v0.3 directory and starting over? On Tue, Jul 21, 2015 at 6:38 PM, Tim Holy tim.h...@gmail.com wrote: Strange. That commit is present in the repository: see https://github.com/timholy/HDF5.jl/commits/master Anyone else having the same problem? I just did this and it went off without a hitch (julia-old is my installation of the 0.3 release): $ mkdir /tmp/packages $ JULIA_PKGDIR=/tmp/packages julia-old _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_)| Documentation: http://docs.julialang.org _ _ _| |_ __ _ | Type help() for help. | | | | | | |/ _` | | | | |_| | | | (_| | | Version 0.3.7-pre+1 (2015-02-17 22:12 UTC) _/ |\__'_|_|_|\__'_| | Commit d15f183* (153 days old release-0.3) |__/ | x86_64-linux-gnu julia Pkg.init() INFO: Initializing package repository /tmp/packages/v0.3 INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl julia Pkg.add(HDF5) INFO: Cloning cache of BinDeps from git:// github.com/JuliaLang/BinDeps.jl.git INFO: Cloning cache of Blosc from git://github.com/stevengj/Blosc.jl.git INFO: Cloning cache of Compat from git:// github.com/JuliaLang/Compat.jl.git INFO: Cloning cache of HDF5 from git://github.com/timholy/HDF5.jl.git INFO: Cloning cache of SHA from git://github.com/staticfloat/SHA.jl.git INFO: Cloning cache of URIParser from git://github.com/JuliaWeb/URIParser.jl.git INFO: Installing BinDeps v0.3.14 INFO: Installing Blosc v0.1.2 INFO: Installing Compat v0.4.9 INFO: Installing HDF5 v0.5.0 INFO: Installing SHA v0.0.4 INFO: Installing URIParser v0.0.5 INFO: Building Blosc % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 1210 1210 0553 0 --:--:-- --:--:-- --:--:-- 555 0 00 233k0 0 221k 0 --:--:-- 0:00:01 --:--:-- 427k Compiling libblosc... CC blosc.c CC blosclz.c CC shuffle.c LINK libblosc INFO: Building HDF5 INFO: Package database updated julia which went like a charm. Maybe try Pkg.update()? --Tim On Monday, July 20, 2015 10:36:25 PM Roger Herikstad wrote: Hi, For some reason I am unable to add HDF5. Not sure if this is related to the recent change splitting JLD off into its own package. This is the error I got ulia Pkg.add(HDF5) INFO: Updating cache of HDF5... ERROR: Missing package versions (possible metadata misconfiguration): HDF5 v(nothing,v0.5.0) [883165af1cef09980a3d9b1718477579d629754c[1:10]] in wait at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib (repeats 2 times) in wait at task.jl:48 in sync_end at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib in add at pkg/entry.jl:319 in add at pkg/entry.jl:71 in anonymous at pkg/dir.jl:28 in cd at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib in __cd#229__ at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia /sys.dylib in add at pkg.jl:20 This is my versioninfo: julia versioninfo() Julia Version 0.3.10 Commit c8ceeef* (2015-06-24 13:54 UTC) Platform Info: System: Darwin (x86_64-apple-darwin13.4.0) CPU: Intel(R) Xeon(R) CPU X5472 @ 3.00GHz WORD_SIZE: 64 BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn) LAPACK: libopenblas LIBM: libopenlibm LLVM: libLLVM-3.3 I appreciate any advice on what the problem might be. Thanks! -- ~ Roger
Re: [julia-users] Unable to add HDF5
You could try Pkg.rm(HDF5) and then delete the HDF5 directory in ~/.julia/.cache. --Tim On Tuesday, July 21, 2015 06:45:55 PM Roger Herikstad wrote: Hm, just tried Pkg.update() on 0.4.0-dev+5955 and I got the new version of HDF5 without any problems, so there's probably something wonky going on with Pkg on my 0.3.10. Is there anything I can do to try and reset Pkg, short of nuking my whole ~/.julia/v0.3 directory and starting over? On Tue, Jul 21, 2015 at 6:38 PM, Tim Holy tim.h...@gmail.com wrote: Strange. That commit is present in the repository: see https://github.com/timholy/HDF5.jl/commits/master Anyone else having the same problem? I just did this and it went off without a hitch (julia-old is my installation of the 0.3 release): $ mkdir /tmp/packages $ JULIA_PKGDIR=/tmp/packages julia-old _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_)| Documentation: http://docs.julialang.org _ _ _| |_ __ _ | Type help() for help. | | | | | | |/ _` | | | | | | | |_| | | | (_| | | Version 0.3.7-pre+1 (2015-02-17 22:12 UTC) _/ |\__'_|_|_|\__'_| | Commit d15f183* (153 days old release-0.3) |__/ | x86_64-linux-gnu julia Pkg.init() INFO: Initializing package repository /tmp/packages/v0.3 INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl julia Pkg.add(HDF5) INFO: Cloning cache of BinDeps from git:// github.com/JuliaLang/BinDeps.jl.git INFO: Cloning cache of Blosc from git://github.com/stevengj/Blosc.jl.git INFO: Cloning cache of Compat from git:// github.com/JuliaLang/Compat.jl.git INFO: Cloning cache of HDF5 from git://github.com/timholy/HDF5.jl.git INFO: Cloning cache of SHA from git://github.com/staticfloat/SHA.jl.git INFO: Cloning cache of URIParser from git://github.com/JuliaWeb/URIParser.jl.git INFO: Installing BinDeps v0.3.14 INFO: Installing Blosc v0.1.2 INFO: Installing Compat v0.4.9 INFO: Installing HDF5 v0.5.0 INFO: Installing SHA v0.0.4 INFO: Installing URIParser v0.0.5 INFO: Building Blosc % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 1210 1210 0553 0 --:--:-- --:--:-- --:--:-- 555 0 00 233k0 0 221k 0 --:--:-- 0:00:01 --:--:-- 427k Compiling libblosc... CC blosc.c CC blosclz.c CC shuffle.c LINK libblosc INFO: Building HDF5 INFO: Package database updated julia which went like a charm. Maybe try Pkg.update()? --Tim On Monday, July 20, 2015 10:36:25 PM Roger Herikstad wrote: Hi, For some reason I am unable to add HDF5. Not sure if this is related to the recent change splitting JLD off into its own package. This is the error I got ulia Pkg.add(HDF5) INFO: Updating cache of HDF5... ERROR: Missing package versions (possible metadata misconfiguration): HDF5 v(nothing,v0.5.0) [883165af1cef09980a3d9b1718477579d629754c[1:10]] in wait at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib (repeats 2 times) in wait at task.jl:48 in sync_end at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib in add at pkg/entry.jl:319 in add at pkg/entry.jl:71 in anonymous at pkg/dir.jl:28 in cd at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib in __cd#229__ at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib in add at pkg.jl:20 This is my versioninfo: julia versioninfo() Julia Version 0.3.10 Commit c8ceeef* (2015-06-24 13:54 UTC) Platform Info: System: Darwin (x86_64-apple-darwin13.4.0) CPU: Intel(R) Xeon(R) CPU X5472 @ 3.00GHz WORD_SIZE: 64 BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn) LAPACK: libopenblas LIBM: libopenlibm LLVM: libLLVM-3.3 I appreciate any advice on what the problem might be. Thanks!
Re: [julia-users] Unable to add HDF5
Ah, of course. Thanks! It works now. Sorry for the noise. On Tue, Jul 21, 2015 at 6:51 PM, Tim Holy tim.h...@gmail.com wrote: You could try Pkg.rm(HDF5) and then delete the HDF5 directory in ~/.julia/.cache. --Tim On Tuesday, July 21, 2015 06:45:55 PM Roger Herikstad wrote: Hm, just tried Pkg.update() on 0.4.0-dev+5955 and I got the new version of HDF5 without any problems, so there's probably something wonky going on with Pkg on my 0.3.10. Is there anything I can do to try and reset Pkg, short of nuking my whole ~/.julia/v0.3 directory and starting over? On Tue, Jul 21, 2015 at 6:38 PM, Tim Holy tim.h...@gmail.com wrote: Strange. That commit is present in the repository: see https://github.com/timholy/HDF5.jl/commits/master Anyone else having the same problem? I just did this and it went off without a hitch (julia-old is my installation of the 0.3 release): $ mkdir /tmp/packages $ JULIA_PKGDIR=/tmp/packages julia-old _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_)| Documentation: http://docs.julialang.org _ _ _| |_ __ _ | Type help() for help. | | | | | | |/ _` | | | | | | | |_| | | | (_| | | Version 0.3.7-pre+1 (2015-02-17 22:12 UTC) _/ |\__'_|_|_|\__'_| | Commit d15f183* (153 days old release-0.3) |__/ | x86_64-linux-gnu julia Pkg.init() INFO: Initializing package repository /tmp/packages/v0.3 INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl julia Pkg.add(HDF5) INFO: Cloning cache of BinDeps from git:// github.com/JuliaLang/BinDeps.jl.git INFO: Cloning cache of Blosc from git:// github.com/stevengj/Blosc.jl.git INFO: Cloning cache of Compat from git:// github.com/JuliaLang/Compat.jl.git INFO: Cloning cache of HDF5 from git://github.com/timholy/HDF5.jl.git INFO: Cloning cache of SHA from git:// github.com/staticfloat/SHA.jl.git INFO: Cloning cache of URIParser from git://github.com/JuliaWeb/URIParser.jl.git INFO: Installing BinDeps v0.3.14 INFO: Installing Blosc v0.1.2 INFO: Installing Compat v0.4.9 INFO: Installing HDF5 v0.5.0 INFO: Installing SHA v0.0.4 INFO: Installing URIParser v0.0.5 INFO: Building Blosc % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 1210 1210 0553 0 --:--:-- --:--:-- --:--:-- 555 0 00 233k0 0 221k 0 --:--:-- 0:00:01 --:--:-- 427k Compiling libblosc... CC blosc.c CC blosclz.c CC shuffle.c LINK libblosc INFO: Building HDF5 INFO: Package database updated julia which went like a charm. Maybe try Pkg.update()? --Tim On Monday, July 20, 2015 10:36:25 PM Roger Herikstad wrote: Hi, For some reason I am unable to add HDF5. Not sure if this is related to the recent change splitting JLD off into its own package. This is the error I got ulia Pkg.add(HDF5) INFO: Updating cache of HDF5... ERROR: Missing package versions (possible metadata misconfiguration): HDF5 v(nothing,v0.5.0) [883165af1cef09980a3d9b1718477579d629754c[1:10]] in wait at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib (repeats 2 times) in wait at task.jl:48 in sync_end at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib in add at pkg/entry.jl:319 in add at pkg/entry.jl:71 in anonymous at pkg/dir.jl:28 in cd at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib in __cd#229__ at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/jul ia /sys.dylib in add at pkg.jl:20 This is my versioninfo: julia versioninfo() Julia Version 0.3.10 Commit c8ceeef* (2015-06-24 13:54 UTC) Platform Info: System: Darwin (x86_64-apple-darwin13.4.0) CPU: Intel(R) Xeon(R) CPU X5472 @ 3.00GHz WORD_SIZE: 64 BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn) LAPACK: libopenblas LIBM: libopenlibm LLVM: libLLVM-3.3 I appreciate any advice on what the problem might be. Thanks! -- ~ Roger
[julia-users] Unable to add HDF5
Hi, For some reason I am unable to add HDF5. Not sure if this is related to the recent change splitting JLD off into its own package. This is the error I got ulia Pkg.add(HDF5) INFO: Updating cache of HDF5... ERROR: Missing package versions (possible metadata misconfiguration): HDF5 v(nothing,v0.5.0) [883165af1cef09980a3d9b1718477579d629754c[1:10]] in wait at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia/sys.dylib (repeats 2 times) in wait at task.jl:48 in sync_end at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia/sys.dylib in add at pkg/entry.jl:319 in add at pkg/entry.jl:71 in anonymous at pkg/dir.jl:28 in cd at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia/sys.dylib in __cd#229__ at /home/roger/Applications/Julia-0.3.10.app/Contents/Resources/julia/lib/julia/sys.dylib in add at pkg.jl:20 This is my versioninfo: julia versioninfo() Julia Version 0.3.10 Commit c8ceeef* (2015-06-24 13:54 UTC) Platform Info: System: Darwin (x86_64-apple-darwin13.4.0) CPU: Intel(R) Xeon(R) CPU X5472 @ 3.00GHz WORD_SIZE: 64 BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn) LAPACK: libopenblas LIBM: libopenlibm LLVM: libLLVM-3.3 I appreciate any advice on what the problem might be. Thanks!
