binaries version of VPF-class

[jiee1993]

Hi, I‘m interested in your work to classify virus sequence using VPF family, but it's difficult for me to install stack in my machine. So I will glad and convenient to use VPF-class if you have binaries version released. Thanks.

[limeng849]

I met the same problem, too. I just downloaded the stack from the official website, but I met the same issue with using the command "curl -sSL https://get.haskellstack.org/ | sh" is that the "Failed to connect to raw.githubusercontent.com port 443: Connection refused" maybe that is because of the internet or can we install the software via Conda?

[KimBioInfoStudio]

hello guys, could u try this 1st https://github.com/commercialhaskell/stack/releases

[jiee1993]

yes, I have installed stack, but still can not install VPF-class using stack build: Exception while reading snapshot from https://raw.githubusercontent.com/commercialhaskell/stackage-snapshots/master/nightly/2020/9/23.yaml: HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [("User-Agent","Haskell pantry package")] path = "/commercialhaskell/stackage-snapshots/master/nightly/2020/9/23.yaml" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 } (InternalException (HostCannotConnect "raw.githubusercontent.com" [Network.Socket.connect: <socket: 13>: does not exist (Connection refused)]))

[bielr]

Hi @jiee1993,

Does the issue persist? That sounds like either a temporary issue with github/stack or your network connection.

[jiee1993]

Emm, still filled to build stack in the public server cluster without root right in China. But I succeed install stack and VPF-class in my windows subsystem (need update wsl to wsl2) at the expense of running speed.

[bielr]

Sorry, I haven't been able to reproduce your issue. Meanwhile, I prepared a static build (MPI is disabled) of the current version that you can download here: https://bioinfo.uib.es/~recerca/VPF-Class/build/vpf-class-x86_64-linux@dd88a543f28eb339cf0dcb89f34479c84b3a8056

Hope this helps

[jiee1993]

Much thanks for packing the binary version, It runs smoothly in the server.

[limeng849]

hey, bier, I still stuck in the stack compilations, it still occurs this problem even I add some configuration in the ~/.stack/config.yaml file according to the stack official suggestion😩. And could you provide more details about how to use the static build file because I downloaded it but sounds can't work on my MAC directly. Thank you ! Below are the same issue in stack build: Exception while reading snapshot from https://raw.githubusercontent.com/commercialhaskell/stackage-snapshots/master/nightly/2020/9/23.yaml: HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [("User-Agent","Haskell pantry package")] path = "/commercialhaskell/stackage-snapshots/master/nightly/2020/9/23.yaml" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } (InternalException (HandshakeFailed (Error_Misc "Network.Socket.recvBuf: resource vanished (Connection reset by peer)")))

[bielr]

Sorry for the delay.

The static build is linux only, it won't work on a Mac.

That download error must be related to your computer. Could you please check if that file (https://raw.githubusercontent.com/commercialhaskell/stackage-snapshots/master/nightly/2020/9/23.yaml) is downloadable for you?

[mengyan-zhou]

Hi， when I used the command " stack build", there were errors as following: -- While building package cryptonite-0.27 (scroll up to its section to see the error) using: /home/Visit/.stack/setup-exe-cache/x86_64-linux/Cabal-simple_mPHDZzAJ_3.2.0.0_ghc-8.10.2 --builddir=.stack-work/dist/x86_64-linux/Cabal-3.2.0.0 build --ghc-options " -fdiagnostics-color=always" Process exited with code: ExitFailure 1

Could you tell me how to deal with these? thanks in advance!

[bielr]

Could you provide the full output? Looks like there was a problem building cryptonite (a dependency)

[mengyan-zhou]

Hi， Thanks for your reply! the following image was the full output.

[bielr]

Hi,

Apparently you are using an old GCC version (< 4.9). If an upgrade is not feasible, you could try adding the following to stack.yaml:

flags:
  cryptonite:
    use_target_attributes: false

Hope that helps

[mengyan-zhou]

Hi， when I used the command " stack build", there were errors as following. I wonder if you could help me solve this problem.

[bielr]

That's an easier one! You should make sure that the gmp-devel package is installed.

[bielr]

We now provide a Docker image (see the README) which includes a pre-built binary and a script to automatically download data files, so I'd consider this fixed.