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

[HijaziHassan]

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'

• removing 'C:/Users/Space Pack/Documents/R/win-library/4.2/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]

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]

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.

.

[lgatto]

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]

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

[lgatto]

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