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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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ERROR: compilation failed for package ‘mzR’ (centos7/R 4.3.1) #286

Open ddafeng opened 8 months ago

ddafeng commented 8 months ago

In file included from ./boost/regex.hpp:28:0, from boost/libs/regex/src/posix_api.cpp:22: ./boost/regex/config.hpp:189:43: 致命错误：boost/regex/config/cwchar.hpp：没有那个文件或目录

include <boost/regex/config/cwchar.hpp>

                                       ^

编译中断。 make: *** [boost/libs/regex/src/posix_api.o] 错误 1 ERROR: compilation failed for package ‘mzR’

sneumann commented 8 months ago

Hi ddafeng, thanks for reporting. which compiler are you using here, is that gcc or clang ? I also don't understand the chinese, is my guess correct that the compiler says it can't find cwchar.hpp ? Yours, Steffen

sneumann commented 8 months ago

I added the missing file in 5143a8f59a99db7c8c1f93af5f7d3cf5d5ea2552, but I can't test if others are missing. Could you check if the github devel version in https://github.com/sneumann/mzR compiles on your setup ? Thanks, Yours, Steffen

ddafeng commented 8 months ago

Thank you for your reply, I tried a lot to solve the problem, and finally I was able to install mzR in centos 7 with the help of the Anaconda platform. Anaconda is a good R package and Python package management platform that solves the problem of missing dependencies. Of course, I also tried to find a possible reason for the missing dependency files, and I guessed that there might be a problem with the Boost inventory under the BH package, but I didn't know much about it, so I didn't find the root cause. I apologize for not being able to provide you with valuable advice.

谢谢您的回复，为解决问题我做了跟多的尝试，最终我借助Anaconda平台在centos7中完成了mzR的安装。Anaconda是一个比较不错的R包和Python包管理平台，解决了依赖缺失的问题。当然中途我也尝试寻找依赖文件缺失的可能原因，我猜测可能是BH包下的Boost库存在问题，然而我对此不太了解，因此我也没有发现根本的原因。无法为您提供有价值的建议我很抱歉。

发件人: Steffen @.> 发送时间: 2023年11月3日 15:36 收件人: @.> 抄送: @.>; @.> 主题: Re: [sneumann/mzR] ERROR: compilation failed for package ‘mzR’ (centos7/R 4.3.1) (Issue #286)

I added the missing file in 5143a8fhttps://github.com/sneumann/mzR/commit/5143a8f59a99db7c8c1f93af5f7d3cf5d5ea2552, but I can't test if others are missing. Could you check if the github devel version in https://github.com/sneumann/mzR compiles on your setup ? Thanks, Yours, Steffen

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sneumann commented 8 months ago

Hi, thanks for reporting back. Just for the record, the boost BH package is not used, since (last time I checked) it has the header files and does not include everything we'd need in mzR (specifically, the compiled libraries). That anaconda works could mean that this packaging uses a different compiler, language environment or R version. So I won't merge the PR until someone confirms that it solves an issue. Yours, Steffen