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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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installation of package ‘mzR’ had non-zero exit status #255

Open HijaziHassan opened 2 years ago

HijaziHassan commented 2 years ago

I am trying to compile the mzR package, but always getting this error after running the code below.

if (!requireNamespace("BiocManager", quietly=TRUE))
  install.packages("BiocManager")
BiocManager::install("mzR", suppressUpdates = TRUE)

. . . ERROR: compilation failed for package 'mzR'

The downloaded source packages are in ‘C:\Users\Space Pack\AppData\Local\Temp\RtmpyAcC0R\downloaded_packages’ Warning message: In .inet_warning(msg) : installation of package ‘mzR’ had non-zero exit status

You mentioned that packages: 1-brew 2- install 3- netcdf

are pre-requisites. I tried to install netcd using the following code:

BiocManager::install("netcdf")

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.16), R Under development (unstable) (2021-12-11 r81350) Installing package(s) 'netcdf' Warning messages: 1: R graphics engine version 15 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. 2: In .inet_warning(msg) : package ‘netcdf’ is not available for Bioconductor version '3.15'

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages

I tried: install.packages()

it only worked for brew.

could you help here please?

lgatto commented 2 years ago
  1. You message is ill-formatted and makes it difficult to see what you have tried.
  2. You need to install the ncdf4 package, which depends on a system netcdf system dependency.
  3. Please always provide you session info when reporting issues.
HijaziHassan commented 2 years ago

Hi Laurent, I agree. 1- I took a screenshot. I hope it helps. 2- already installed (check the attached image). 3- Noted. check the attached image.

Thank you in advance.

mzR_error .

lgatto commented 2 years ago

You run into issues because you try to install from source - and this happens there currently aren't any binaries for windows for devel.

My only suggestion is (1) use release, or (2) wait until this is sorted out or (3) battle with compilation on windows (not advised).

HijaziHassan commented 2 years ago

Thanks Laurent. Maybe it is a naïve question: But what do you mean by "use release"?

lgatto commented 2 years ago

You use R-devel and hence Bioc devel. If you use the latest stable R, you'll get the stable Bioc release.