windows install

[dgcovell]

CANNOT GET A CLEAN INSTALL. (NOTE MY RESPONSES WILL BE IN CAPS)

https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

source("https://raw.githubusercontent.com/rickhelmus/patRoon/master/install_patRoon.R") Run installPatRoon() to start the installation installPatRoon()

This installation script will install the patRoon R package. The code uses some functions and other code from the installr package (https://github.com/talgalili/installr) Credits go to its authors.

Installation configuration:

• what: mandatory_packages, optional_packages, tools, deps, patRoon
• Installation path for external dependencies: ~/patRoon-install
• Install patRoon example data: TRUE

NOTE: It is best to run this in a fresh R session! patRoon and its R package dependencies can either be installed from regular repositories (CRAN, BioConductor) or from the patRoonDeps repository. The former ensures that you will always get the latest package versions. On the other hand, using the patRoonDeps repository minimizes the risk on installation errors. Furthermore, when using the patRoonDeps repository you can choose to use a local R library which is only used if specified explicitly and will therefore not interfere with your current installed packages. NOTE: patRoonDeps only work with recent versions of R. (From) Where do you want to install patRoon and its dependencies? If unsure, choose 1.

1: Install from patRoonDeps repository (inside an isolated R library) 2: Install from patRoonDeps repository (inside your default R library) 3: Install from standard repositories (CRAN, BioConductor, GitHub)

Selection: 3

Pre-Installing mandatory R dependencies...

The following mandatory packages will be installed: installr, mzR, xcms, CAMERA Installing packages: installr

EXECUTE: install.packages("installr")

DOWNLOADS APPEAR TO GO FINE.

Installing external dependencies...

---

Pre-Installing optional R dependencies...

Which of the following R packages do you want to install?

1: KPIC2 (algorithm to find/group features) 2: RAMClustR (algorithm for componentization) 3: nontarget (algorithm for componentization of homologous series) 4: cliqueMS (algorithm for componentization) 5: MetaClean (to calculate chromatographic peak qualities) 6: RDCOMClient (required for Bruker DataAnalysis integration) 7: All

Enter one or more numbers separated by spaces and then ENTER, or 0 to cancel 1: 7

WHICH GETS ME TO HERE:

C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o KPIC.dll tmp.def RcppExports.o getPIP.o getPIP_kmeans.o groupCandidate.o peak_detection.o -LC:/Users/covelld/DOCUME~1/R/R-41~1.0/bin/x64 -lR installing to C:/Users/covelld/Documents/R/R-4.1.0/library/00LOCK-KPIC/00new/KPIC/libs/x64 R byte-compile and prepare package for lazy loading Warning in fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.9). This might lead to errors when loading mzR. If you encounter such issues, please send a report, including the output of sessionInfo() to the Bioc support forum at https://support.bioconductor.org/. For details see also https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue. Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace 'vctrs' 0.5.1 is already loaded, but >= 0.5.2 is required Calls: ... asNamespace -> loadNamespace -> namespaceImport -> loadNamespace Execution halted

I AM RUNNING R VERSION $.1.0 (2021-05-18)

Any help would be appreciated.

Regards, David

[schymane]

It seems the issue is here: namespace 'vctrs' 0.5.1 is already loaded, but >= 0.5.2 is required

... but I can't tell which R version you have (is the $ a 3 or 4? My keyboard is different)

Are you able to install a newer version of vctrs and does that solve the issue?

[rickhelmus]

Closing this due to inactivity.