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brentp / hts-nim-tools

useful command-line tools written to showcase hts-nim
https://github.com/brentp/hts-nim
MIT License
49 stars 6 forks source link

Installation error #7

Closed pengyu1608 closed 5 years ago

pengyu1608 commented 5 years ago

Hi, I tried to install hts-nim-tools. My operating system is CentOS 7.2.

My procedure:

curl https://nim-lang.org/choosenim/init.sh -sSf | sh export PATH=$PATH:$HOME/.nimble/bin

nimble install -y https://github.com/brentp/hts-nim-tools --nimbleDir:$HOME/.nimble

Downloading https://github.com/brentp/hts-nim-tools using git Verifying dependencies for hts_nim_tools@0.1.5 Info: Dependency on c2nim@>= 0.9.10 already satisfied Verifying dependencies for c2nim@0.9.14 Info: Dependency on docopt@any version already satisfied Verifying dependencies for docopt@0.6.8 Info: Dependency on regex@>= 0.7.4 already satisfied Verifying dependencies for regex@0.12.0 Info: Dependency on unicodedb@>= 0.7.2 already satisfied Verifying dependencies for unicodedb@0.7.2 Info: Dependency on unicodeplus@>= 0.5.0 already satisfied Verifying dependencies for unicodeplus@0.5.1 Info: Dependency on unicodedb@>= 0.7 already satisfied Verifying dependencies for unicodedb@0.7.2 Info: Dependency on lapper@any version already satisfied Verifying dependencies for lapper@0.1.4 Info: Dependency on hts@any version already satisfied Verifying dependencies for hts@0.2.21 Info: Dependency on kexpr@any version already satisfied Verifying dependencies for kexpr@0.0.2 Installing hts_nim_tools@0.1.5 Building hts_nim_tools/hts_nim_tools using c backend Error: Build failed for package: hts_nim_tools ... Details: ... Execution failed with exit code 1 ... Command: "/home/yupeng/.nimble/bin/nim" c --noBabelPath -d:release --path:"/home/yupeng/.nimble/pkgs/c2nim-0.9.14" --path:"/home/yupeng/.nimble/pkgs/docopt-0.6.8" --path:"/home/yupeng/.nimble/pkgs/regex-0.12.0" --path:"/home/yupeng/.nimble/pkgs/unicodedb-0.7.2" --path:"/home/yupeng/.nimble/pkgs/unicodeplus-0.5.1" --path:"/home/yupeng/.nimble/pkgs/unicodedb-0.7.2" --path:"/home/yupeng/.nimble/pkgs/lapper-0.1.4" --path:"/home/yupeng/.nimble/pkgs/hts-0.2.21" --path:"/home/yupeng/.nimble/pkgs/kexpr-0.0.2" -o:"/tmp/nimble_39277/githubcom_brentphtsnimtools/hts_nim_tools" "/tmp/nimble_39277/githubcom_brentphtsnimtools/src/hts_nim_tools.nim" ... Output: Hint: used config file '/home/yupeng/.choosenim/toolchains/nim-0.20.2/config/nim.cfg' [Conf]

... Hint: util [Processing] ... Hint: kexpr [Processing] ... Hint: version [Processing] ... Hint: lapper [Processing] ... /tmp/nimble_23162/githubcom_brentphtsnimtools/src/count_reads.nim(73, 19) Error: attempting to call undeclared routine: 'querys'

brentp commented 5 years ago

thanks for reporiting. this was do to using a deprecated (and now removed querys function) I have updated the code and it works now.

pengyu1608 commented 5 years ago

Thanks for the reply. It is solved now.

Peng Yu, Ph.D Computational Biologist Laboratory of Stem Cell and Epigenetics State Key Laboratory of Cardiovascular Disease Fuwai Hospital, Chinese Academy of Medical Science 167 Beilishi Road, Beijing, China 100037

From: Brent Pedersen Date: 2019-09-18 20:17 To: brentp/hts-nim-tools CC: Peng Yu; Author Subject: Re: [brentp/hts-nim-tools] Installation error (#7) thanks for reporiting. this was do to using a deprecated (and now removed querys function) I have updated the code and it works now. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.