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Cheng Nuo
@C3iX2
julia> using BioAlignments
[ Info: Precompiling BioAlignments [00701ae9-d1dc-5365-b64a-a3a3ebf5695e]
┌┌ Warning: `@gc_preserve` is deprecated, use `GC.@preserve` instead.
││   caller = include at boot.jl:317 [inlined]
└└ @ Core .\boot.jl:317
┌┌ Warning: `using A: B` will only be allowed for single bindings, not modules.
Use `using A.B` instead
││   caller = ip:0x0
└└ @ Core :-1
ERROR: LoadError: CodecZlib.jl is not installed properly, run Pkg.build("CodecZlib") and restart Julia.
But when I using BioAlignments It will mention the CodecZLib
Ben J. Ward
@BenJWard
What happens when you run Pkg.build("CodecZlib")?
Cheng Nuo
@C3iX2
julia> Pkg.build("CodecZlib")
  Building CodecZlib →→ `C:\Users\Administrator\.julia\packages\CodecZlib\wwgbh\
deps\build.log`
┌┌ Error: Error building `CodecZlib`:
││ ┌┌ Warning: platform_key() is deprecated, use platform_key_abi() from now on
││ ││   caller = ip:0x0
││ └└ @ Core :-1
││ [ Info: Downloading https://github.com/bicycle1885/ZlibBuilder/releases/downl
oad/v1.0.2/Zlib.v1.2.11.x86_64-w64-mingw32.tar.gz to C:\Users\Administrator\.jul
ia\packages\CodecZlib\wwgbh\deps\usr\downloads\Zlib.v1.2.11.x86_64-w64-mingw32.t
ar.gz...
││ ERROR: LoadError: Could not download https://github.com/bicycle1885/ZlibBuild
er/releases/download/v1.0.2/Zlib.v1.2.11.x86_64-w64-mingw32.tar.gz to C:\Users\A
dministrator\.julia\packages\CodecZlib\wwgbh\deps\usr\downloads\Zlib.v1.2.11.x86
_64-w64-mingw32.tar.gz:
││ ErrorException("")
││ Stacktrace:
││  [1] error(::String) at .\error.jl:33
││  [2] macro expansion at .\logging.jl:313 [inlined]
││  [3] #download#93(::Bool, ::Function, ::String, ::String) at C:\Users\Adminis
trator\.julia\packages\BinaryProvider\1nGWd\src\PlatformEngines.jl:487
││  [4] #download at .\none:0 [inlined]
││  [5] #download_verify#94(::Bool, ::Bool, ::Bool, ::Function, ::String, ::Stri
ng, ::String) at C:\Users\Administrator\.julia\packages\BinaryProvider\1nGWd\src
\PlatformEngines.jl:567
││  [6] #download_verify at .\none:0 [inlined]
││  [7] #install#133(::Prefix, ::String, ::Bool, ::Bool, ::Bool, ::Function, ::S
tring, ::String) at C:\Users\Administrator\.julia\packages\BinaryProvider\1nGWd\
src\Prefix.jl:314
││  [8] (::getfield(BinaryProvider, Symbol("#kw##install")))(::NamedTuple{(:pref
ix, :force, :verbose),Tuple{Prefix,Bool,Bool}}, ::typeof(install), ::String, ::S
tring) at .\none:0
││  [9] top-level scope at C:\Users\Administrator\.julia\packages\CodecZlib\wwgb
h\deps\build.jl:88
││  [10] include at .\boot.jl:317 [inlined]
││  [11] include_relative(::Module, ::String) at .\loading.jl:1038
││  [12] include(::Module, ::String) at .\sysimg.jl:29
││  [13] include(::String) at .\client.jl:398
││  [14] top-level scope at none:0
││ in expression starting at C:\Users\Administrator\.julia\packages\CodecZlib\ww
gbh\deps\build.jl:81
││ ���á�SecurityProtocol��ʱ�����쳣쳣:������ö��ֵ��ЧЧ���޷�����ֵת��Ϊ���͡�Syst
││ em.Net.SecurityProtocolType������ָ������ö��ֵ֮һ��Ȼ�����ԡ����ܵ�ö��ֵΪ��
││ Ssl3��Tls������
││ ����λλ�� ��:1 �ַ�: 35
││ + [System.Net.ServicePointManager]:: <<<< SecurityProtocol =
││     + CategoryInfo          : InvalidOperation: (:) [], RuntimeException
││     + FullyQualifiedErrorId : PropertyAssignmentException
││
││ ʹ�á�2���������á�DownloadFile��ʱ�����쳣쳣:����l���Ѿ��ر�: ����ʱ�����
││ ���
││ ����λλ�� ��:5 �ַ�: 24
││ + $webclient.DownloadFile <<<< ("https://github.com/bicycle1885/ZlibBuilder/r
el
││ eases/download/v1.0.2/Zlib.v1.2.11.x86_64-w64-mingw32.tar.gz", "C:\Users\Admi
ni
││ strator\.julia\packages\CodecZlib\wwgbh\deps\usr\downloads\Zlib.v1.2.11.x86_6
4-
││ w64-mingw32.tar.gz")
││     + CategoryInfo          : NotSpecified: (:) [], MethodInvocationException

││     + FullyQualifiedErrorId : DotNetMethodException
││
└└ @ Pkg.Operations C:\cygwin\home\Administrator\buildbot\worker\package_win64\b
uild\usr\share\julia\stdlib\v0.7\Pkg\src\Operations.jl:1068
Sorry to bother you so much.
Ben J. Ward
@BenJWard
That's strange, it's trying to download a valid version of a zlib binary from the ZLibBuilder release page for mingw32, but just says that it can't.
Cheng Nuo
@C3iX2
yep!!!
Ben J. Ward
@BenJWard
are you able to try julia 1.0 and add BioAllignments in a fresh package environment?
Cheng Nuo
@C3iX2
I’ll try it.thanks
Cheng Nuo
@C3iX2
I Update the powershell from 2.0 to 3.0 fixes the CodecZlib building error .It finally works.Thank you for your advice!
XD
Cheng Nuo
@C3iX2

The last question: the rest packages GeneticVariation and Phylogenies still seem not OK

julia> Pkg.add("Phylogenies")
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package Phylogenies [875022e3]:
 Phylogenies [875022e3] log:
 ├├──possible versions are: 0.1.0 or uninstalled
 ├├──restricted to versions * by an explicit requirement, leaving only versions
0.1.0
 └└──restricted by julia compatibility requirements to versions: uninstalled ——no versions left
julia> Pkg.add("GeneticVariation")
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package GeneticVariation [9bc6ac9
d]:
 GeneticVariation [9bc6ac9d] log:
 ├├──possible versions are: [0.1.0, 0.2.0, 0.3.0-0.3.2] or uninstalled
 ├├──restricted to versions * by an explicit requirement, leaving only versions
[0.1.0, 0.2.0, 0.3.0-0.3.2]
 ├├──restricted by compatibility requirements with BioSequences [7e6ae17a] to ve
rsions: [0.2.0, 0.3.0-0.3.2] or uninstalled, leaving only versions: [0.2.0, 0.3.
0-0.3.2]
 ││ └└──BioSequences [7e6ae17a] log:
 ││   ├├──possible versions are: [0.5.0, 0.6.0-0.6.3, 0.7.0, 0.8.0-0.8.3, 1.0.0]
 or uninstalled
 ││   └└──restricted to versions 1.0.0 by an explicit requirement, leaving only
versions 1.0.0
 └└──restricted by julia compatibility requirements to versions: uninstalled ——no versions left

How to deal with it?Thanks again!

julia> versioninfo()
Julia Version 1.0.1
Commit 0d713926f8 (2018-09-29 19:05 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM) i5-4200M CPU @ 2.50GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, haswell)
Ben J. Ward
@BenJWard
GeneticVariation does not have a v0.7/v1.0 release just yet, although the master branch of GeneticVariation should work. I've made the changes, just didnt get around to tagging a release yet. I will do it tomorrow.
Cheng Nuo
@C3iX2
OK looking forward to the release!
Kevin Bonham
@kescobo
@BenJWard Would you enable travis on MicrobiomePlots.jl and BiobakeryUtils.jl? I don't seem to have permission
Or else give me permission if that's possible
Ben J. Ward
@BenJWard
@kescobo That's odd, you are listed as having admin permissions on those two repositories?
I've turned travis on for both of them, your mileage may vary currently though, what with the recent github issues.
Kevin Bonham
@kescobo
@BenJWard I saw that, thanks! I just tagged the first releases and attobot isn't even responding either. We'll see what happens when stuff comes back online
I see that I have admin, and I was able to add attobot for example. It might just be my unfamiliarity with travis/codecov, but I couldn't find those repos when I tried to enable it (though I could see Microbiome.jl and all of my own repos)
Kevin Bonham
@kescobo

@BenJWard One more - can you enable codecov as well?
https://github.com/BioJulia/MicrobiomePlots/settings/installations
https://github.com/BioJulia/BiobakeryUtils.jl/settings/installations

It seems I need to have admin "on the organization that owns the repository" rather than on the repo itself for some reason. Odd that some integrations don't require that (I was able to do appveyor fine)

Screen Shot 2018-10-24 at 16.04.26.png
Or actually - maybe it's already enabled... it seems like it's queued. So maybe there's nothing to do
Ben J. Ward
@BenJWard
Yeah codecov tends to "just work" if it gets pushed coverage info about a package. Which is handy!
ZxyChopcat
@ZxyChopcat
Hi! I followed Cheng Nuo here.I'm looking forward to the new release and want to know when will it be released.No offence.Thank you!
Jonathan Bieler
@jonathanBieler
Need any help to update Bio.jl to v0.7 ? It looks like most packages are working already.
Mateusz Kaduk
@matkad_gitlab
Whats the status of BioJulia now? I am trying to use Bio.Seq to read fastq files, but it seems its not working with 1.0.x
there also seems to be BioSequences package, is there a reason why they're not under the same umbrella but separate? :)
Joe Greener
@jgreener64
Bio.jl is an umbrella package that collects and re-exports other packages from the BioJulia ecosystem, e.g. Bio.Seq is just the BioSequences package.
Most of the individual packages work and can be used now on v0.7/v1.0.x.
Bio.jl still needs a bit of work, or perhaps just a release tagged. I think @BenJWard was working on that but of course PRs are very welcome.
Mateusz Kaduk
@matkad_gitlab
@jgreener64 thanks Joe, I have another question, I am using Juno/Emacs and in both cases I dont see completion for FASTQ modules inside BioSequences. Is that expected? Do you know IDE that can show available modules/functions from packages?
Joe Greener
@jgreener64
I think the Julia plugin for VScode can do something like this, see https://github.com/JuliaEditorSupport/julia-vscode/wiki/IntelliSense.
You might also get more info on the Julia Gitter, the Julia Slack, or Discourse.
Christopher Rackauckas
@ChrisRackauckas
apropos("PackageName")
Mateusz Kaduk
@mateusz-kaduk_gitlab
@BenJWard Hey Ben, is there a reason why Pkg.clone("https://github.com/BioJulia/Bio.jl.git") is fixed to 1.0.0 version, would it be possible to relax requirement a bit to have it 1.0.x ? :)
When I try to install on 1.0.2 I get something like this
restricted to versions 1.0.0 by an explicit requirement — no versions left
Thanks! :)
Scott McCain
@jspmccain
Hey! Just wondering if anybody here is using Julia for proteomics?
kdyrhage
@kdyrhage
@jspmccain To some extent
Ben J. Ward
@BenJWard
Last time I had a go at testing Bio.jl, with the aim of tagging a release, BioServices.jl was not passing all tests. I'm not sure if this was fixed yet, I'll try again (I test locally with Bio.jl because of the number of packages it has to test means travis stops).
Ben J. Ward
@BenJWard
@/all Can I please ask everyone that any conversations and questions that are generic in nature and not specific to the BioJulia/Bio.jl exactly, take place over at https://gitter.im/BioJulia/General instead.
@/all I'm sutting down the Discord server in favour of the creation of a General Gitter room, for general Q&A and chat, and then a series of package specific rooms for very detailed Q's about a package, and dev chat. The Discord server has not made my life easier as I hoped it might.
@/all Thank you!
Ivan Dorna
@dorvan
@/all Hello
we are a team who wants to move from R(xcms) usage in omics, especially for untergeted discovery to biojulia
cossio
@cossio
Is it possible to bridge these BioJulia rooms into the Julia slack?
Mateusz Kaduk
@mateusz-kaduk_gitlab
Hi, do you guys know CRAM reader for Julia?
Guillermo Luque
@gluque
Hi there. Is it possible to open a gzipped FASTA using FASTX? I have tried with GzipDecompressorStream from CodecZlib, but not sure how to make the stream readable by FASTA.Reader()
Ciarán O'Mara
@CiaranOMara
@gluque, that seems to be fixed in an unrelease commit.
You can get around this issue by setting up the reader in the following way,
io = open("data/genomic-seq.fasta.gz")
stream = GzipDecompressorStream(io)
reader = FASTA.Reader(FASTA.State(stream, 1, 1, false), nothing)
Guillermo Luque
@gluque
Thanks @CiaranOMara, it works like a charm.