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I'm trying to install a github file through bash following these instructions
https://github.com/allenai/s2orc-doc2json
bash scripts/setup_grobid.sh
but I'm getting the following error
bash scripts/setup_grobid.sh
SYSTEM_WGETRC = c:/progra~1/wget/etc/wgetrc
syswgetrc = c:/progra~1/wget/etc/wgetrc
--2022-07-21 20:55:25-- https://github.com/kermitt2/grobid/archive/0.6.1.zip
Resolving github.com... 140.82.121.4
Connecting to github.com|140.82.121.4|:443... connected.
OpenSSL: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Unable to establish SSL connection.
unzip: cannot find or open 0.6.1.zip, 0.6.1.zip.zip or 0.6.1.zip.ZIP.
rm: cannot remove '0.6.1.zip': No such file or directory
scripts/setup_grobid.sh: line 11: cd: /c/Users/User/grobid-0.6.1: No such file or directory
scripts/setup_grobid.sh: line 12: ./gradlew: No such file or directory
cp: cannot stat '/c/Users/User/git/s2orc-pdf2json/pdf2json/grobid/config.yaml': No such file or directory
cp: cannot stat '/c/Users/User/git/s2orc-pdf2json/pdf2json/grobid/grobid.properties': No such file or directory
scripts/setup_grobid.sh: line 22: ./gradlew: No such file or directory
This is the setup_grobid.sh after running it through ShellCheck.net
#!/usr/bin/env bash
# put in your pdf2json directory here
export PDF2JSON_HOME=$HOME/Desktop/s2orc-doc2json-main
# Download Grobid
cd "$HOME" || exit
wget https://github.com/kermitt2/grobid/archive/0.6.1.zip
unzip 0.6.1.zip
rm 0.6.1.zip
cd "$HOME"/Desktop/s2orc-doc2json-main/grobid-0.6.1 || exit
./gradlew clean install
## Grobid configurations
# increase max.connections to slightly more than number of processes
# decrease logging level
# this isn't necessary but is nice to have if you are processing lots of files
cp "$PDF2JSON_HOME"/pdf2json/grobid/config.yaml "$HOME"/grobid-0.6.1/grobid-service/config/config.yaml
cp "$PDF2JSON_HOME"/pdf2json/grobid/grobid.properties "$HOME"/grobid-0.6.1/grobid-home/config/grobid.properties
## Start Grobid
./gradlew run
I even tried to --no-check-certificate but still got the same error.
edit: I'm using Wget 1.11.4 / OpenSSL 1.1.1q 5 Jul 2022
Telling by
OpenSSL: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
this might be caused by github droping support for ancient TLS version protocols https://github.blog/2018-02-01-crypto-removal-notice/ and a fairly outdated wget+openssl installation.
Try forcing a specific modern TLS protocol and see how it goes
wget --secure-protocol=TLSv1_2 https://github.com/kermitt2/grobid/archive/0.6.1.zip
or try to upgrade your installation
As a rule of thumb, start your scripts with
set -ex
So that they
stop if any instruction fails
echo the instruction that is being executed
Related
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I already installed all neccessary libraries it couldn't found (libxslt-dev, libxml2-dev), specified -- --with-xml2-include=/usr/include/libxml2 --use-system-libraries, but it still fails with
make "DESTDIR=" install
make: /usr/bin/mkdir: Command not found
make: *** [Makefile:202: .sitearchdir.-.nokogiri.time] Error 127
sudo ln -s /bin/mkdir /usr/bin/mkdir
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I am running Ubuntu 18.04. I had rust already installed using the instructions at rustup.rs in my /home/username/.cargo directory. When trying to install deno with:
cargo insall deno
towards the end of the process the build fails with the error:
Compiling deno_core v0.47.0
error[E0599]: no method named `map_or` found for type `std::result::Result<&url::Url, &rusty_v8::data::TryFromTypeError>` in the current scope
--> /home/kaan.atakan/.cargo/registry/src/github.com-1ecc6299db9ec823/deno_core-0.47.0/bindings.rs:569:41
|
569 | v8::String::new(scope, url.as_ref().map_or("<unknown>", Url::as_str))
| ^^^^^^ help: there is a method with a similar name: `map_err`
error: aborting due to previous error
For more information about this error, try `rustc --explain E0599`.
error: could not compile `deno_core`.
warning: build failed, waiting for other jobs to finish...
error: failed to compile `deno v1.0.4`, intermediate artifacts can be found at `/tmp/cargo-installuTtprd`
Caused by:
build failed
Doh! It turns out my rust installation was out of date. I updated it by typing rustup update in to the terminal and after the update was finished I ran cargo install deno again and everything worked!
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dpkg: error processing archive /var/cache/apt/archives/ruby-progressbar_1.10.1-1_all.deb (--unpack):
trying to overwrite '/usr/lib/ruby/vendor_ruby/ruby-progressbar/base.rb', which is also in package ruby-ruby-progressbar 1.6.0-0kali1
Errors were encountered while processing:
/var/cache/apt/archives/ruby-progressbar_1.10.1-1_all.deb
Scanning application launchers
Updating active launchers
Done
E: Sub-process /usr/bin/dpkg returned an error code (1)
Try the below:
dpkg -i --force-overwrite /var/cache/apt/archives/ruby-progressbar_1.10.1-1_all.deb
apt --fix-broken -f install
I am attempting to install Hackage's servant-auth-server package using stack exec install servant-auth-server, which has worked for me with other packages.
However, with servant-auth-server I get an error.
$ stack exec install servant-auth-server
/run/current-system/sw/bin/install: missing destination file operand after 'servant-auth-server'
Try '/run/current-system/sw/bin/install --help' for more information.
What is the cause of this error?
How can I install servant-auth-server?
EDIT
Running the command $ stack install servant-auth-server also does not work as shown below.
$ stack install servant-auth-server
Error: While constructing the build plan, the following exceptions were encountered:
In the dependencies for servant-auth-server-0.3.0.0:
servant-auth must match ==0.2.*, but the stack configuration has no specified version (latest applicable is 0.2.7.0)
Recommended action: try adding the following to your extra-deps in /home/matthew/.stack/global-project/stack.yaml:
- servant-auth-0.2.7.0
You may also want to try the 'stack solver' command
Plan construction failed.
The command likely ought to be stack install servant-auth-server
After a recent change in the repository that I am working, I can no longer build. When trying to run any stack command, such as stack build, I get the following error:
$ stack build
Executable named git not found on path: ["/home/matthew/.stack/snapshots/x86_64-linux-nix/lts-8.23/8.0.2/bin","/nix/store/kikxl1m9gg1rh9yfi9ly9bkl39zdb6z7-postgresql-9.5.6/bin","/nix/store/xczvw3rlvr1ind8s88i7yx0vasl4gzxm-ghc-8.0.2/bin","/nix/store/sxngsdy5y53j8fkb912hbpgamb2bpv5q-patchelf-0.9/bin","/nix/store/9ngvanddznmrbf74cvy0pmrqimk3i56x-paxctl-0.9/bin","/nix/store/c07gdr6cm43j1cphadzafq185k711vx4-coreutils-8.26/bin","/nix/store/7pyzxi7k5l6nym972gi2nq8s9f9b2q0j-findutils-4.6.0/bin","/nix/store/gjwa02cchnj2r69dlqjixjmdn0ws7f1v-diffutils-3.5/bin","/nix/store/xk38vw7z7bfr8173vdwfrfamxqcaj7hi-gnused-4.4/bin","/nix/store/r6s8rcd28wsk4gwviyc93343bq5zwlqq-gnugrep-3.0/bin","/nix/store/bvs3nyfflhsb75cfn4ff2a6xnksdzx9f-gawk-4.1.3/bin","/nix/store/g3skr3kss1fqqzl5viyg178qbcp4cdky-gnutar-1.29/bin","/nix/store/kdx0bwfy20q6blpgpdb7psbn1y435r56-gzip-1.8/bin","/nix/store/f2fg211g8zy5k624dwx0g7z32cm148mr-bzip2-1.0.6.0.1-bin/bin","/nix/store/adjkz7lhgvl3y3hpkzfsmpk15f0jrnmr-gnumake-4.2.1/bin","/nix/store/lpk84rsbha199vm3k54498lqv2jswqj8-bash-4.4-p5/bin","/nix/store/1hdv6h68f7xy9k0lhxqf26saz0w0r39i-patch-2.7.5/bin","/nix/store/vkbh4xbgxvx3v9813d4kdwv8ggwrp038-xz-5.2.2-bin/bin"]
It seems that my stack program does not know the correct path to my git program.
How can I specify my git path to stack?
I have verified that I do have git installed at the following path.
$ which git
/nix/var/nix/profiles/default/bin/git
I am on nixos 17.03.
Edit.
I am sure that the stack build and which git commands were run in the same environment as they were run back to back in the same shell.
My path is
$ echo $PATH
/home/matthew/bin:/run/wrappers/bin:/run/wrappers/bin:/home/matthew/.nix-profile/bin:/home/matthew/.nix-profile/sbin:/home/matthew/.nix-profile/lib/kde4/libexec:/nix/var/nix/profiles/default/bin:/nix/var/nix/profiles/default/sbin:/nix/var/nix/profiles/default/lib/kde4/libexec:/run/current-system/sw/bin:/run/current-system/sw/sbin:/run/current-system/sw/lib/kde4/libexec
This shows the /nix/var/nix/profiles/default/bin is in the path, which contains git.
Also, in my stack.yaml file when I set system-ghc: true I get an 'access rights' error instead of the 'Executable named git not found' error.
$ stack build
Warning: /home/matthew/backup/azara_work/platform/api/stack.yaml: Unrecognized field in NixOptsMonoid: system-ghc
Cloning into '/home/matthew/backup/azara_work/platform/api/.stack-work/downloaded/4FnxEtHDACVR'...
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
Process exited with ExitFailure 128: /nix/var/nix/profiles/default/bin/git clone --recursive git#github.com:seanhess/rollbar-haskell.git /home/matthew/backup/azara_work/platform/api/.stack-work/downloaded/4FnxEtHDACVR
Add this to either ~/.stack/config.yaml
or local stack.yaml (if it already has a nix: block)
nix:
enable: true
packages: [git]