Cannot install package

[mbell145]

I have xcms installed and I am running RStudio as admin, but I keep receiving the following messages: `> library(devtools) Loading required package: usethis Warning messages: 1: package ‘devtools’ was built under R version 4.0.4 2: package ‘usethis’ was built under R version 4.0.4

install_github("jcapelladesto/geoRge") Downloading GitHub repo jcapelladesto/geoRge@HEAD Skipping 1 packages not available: xcms √ checking for file 'C:\Users\madis\AppData\Local\Temp\RtmpgTGnAD\remotes374462ce7705\jcapelladesto-geoRge-450f8df/DESCRIPTION' ...

• preparing 'geoRge': √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'geoRge_1.0.tar.gz'

Installing package into ‘C:/Users/madis/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified)

• installing source package 'geoRge' ... using staged installation R ** data * moving datasets to lazyload DB Warning in fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.5) than is installed on your system (1.0.6). 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. Warning: namespace 'xcms' is not available and has been replaced by .GlobalEnv when processing object 'mtbls213' Warning: namespace 'xcms' is not available and has been replaced by .GlobalEnv when processing object 'mtbls213' inst ** byte-compile and prepare package for lazy loading Error: (converted from warning) package 'Rcpp' was built under R version 4.0.4 Execution halted ERROR: lazy loading failed for package 'geoRge'
• removing 'C:/Users/madis/Documents/R/win-library/4.0/geoRge' Error: Failed to install 'geoRge' from GitHub: (converted from warning) installation of package ‘C:/Users/madis/AppData/Local/Temp/RtmpgTGnAD/file37446bb523b4/geoRge_1.0.tar.gz’ had non-zero exit status

  traceback() 10: stop(remote_install_error(remotes[[i]], e)) 9: value[3L] 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 6: tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) { stop(remote_install_error(remotes[[i]], e)) }) 5: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual, build_vignettes = build_vignettes, repos = repos, type = type, ...) 4: force(code) 3: withr::with_path(rtools_path(), code) 2: pkgbuild::with_build_tools({ ellipsis::check_dots_used(action = getOption("devtools.ellipsis_action", rlang::warn)) { remotes <- lapply(repo, github_remote, ref = ref, subdir = subdir, auth_token = auth_token, host = host) install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual, build_vignettes = build_vignettes, repos = repos, type = type, ...) } }, required = FALSE) 1: install_github("jcapelladesto/geoRge")`

Any advice on how to continue?

[jcapelladesto]

It is probably related to the "xcms" dependency. Please try to run: `if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("xcms")`

If you had xcms already installed please, copy and paste the result of sessionInfo()

[mbell145]

So I have xcms installed and can access it using library(), so here are the results from sessionInfo(): `> sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods
[9] base

other attached packages: [1] devtools_2.3.2 usethis_2.0.1 xcms_3.12.0 MSnbase_2.15.7
[5] ProtGenerics_1.22.0 S4Vectors_0.28.1 mzR_2.24.1 Rcpp_1.0.6
[9] BiocParallel_1.24.1 Biobase_2.50.0 BiocGenerics_0.36.0

loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.58.0
[3] fs_1.5.0 doParallel_1.0.16
[5] RColorBrewer_1.1-2 rprojroot_2.0.2
[7] GenomeInfoDb_1.26.4 tools_4.0.3
[9] utf8_1.2.1 R6_2.5.0
[11] affyio_1.60.0 DBI_1.1.1
[13] colorspace_2.0-0 withr_2.4.1
[15] tidyselect_1.1.0 prettyunits_1.1.1
[17] processx_3.4.5 curl_4.3
[19] compiler_4.0.3 MassSpecWavelet_1.56.0
[21] preprocessCore_1.52.1 cli_2.3.1
[23] desc_1.3.0 DelayedArray_0.16.3
[25] scales_1.1.1 DEoptimR_1.0-8
[27] robustbase_0.93-7 affy_1.68.0
[29] callr_3.5.1 digest_0.6.27
[31] XVector_0.30.0 pkgconfig_2.0.3
[33] sessioninfo_1.1.1 MatrixGenerics_1.2.1
[35] fastmap_1.1.0 limma_3.46.0
[37] rlang_0.4.10 rstudioapi_0.13
[39] impute_1.64.0 generics_0.1.0
[41] mzID_1.28.0 dplyr_1.0.5
[43] RCurl_1.98-1.3 magrittr_2.0.1
[45] GenomeInfoDbData_1.2.4 MALDIquant_1.19.3
[47] Matrix_1.3-2 munsell_0.5.0
[49] fansi_0.4.2 MsCoreUtils_1.2.0
[51] lifecycle_1.0.0 vsn_3.58.0
[53] MASS_7.3-53.1 SummarizedExperiment_1.20.0 [55] zlibbioc_1.36.0 pkgbuild_1.2.0
[57] plyr_1.8.6 grid_4.0.3
[59] crayon_1.4.1 lattice_0.20-41
[61] ps_1.6.0 pillar_1.5.1
[63] GenomicRanges_1.42.0 codetools_0.2-18
[65] pkgload_1.2.0 XML_3.99-0.6
[67] glue_1.4.2 remotes_2.2.0
[69] pcaMethods_1.82.0 BiocManager_1.30.10
[71] vctrs_0.3.6 foreach_1.5.1
[73] testthat_3.0.2 gtable_0.3.0
[75] RANN_2.6.1 purrr_0.3.4
[77] assertthat_0.2.1 cachem_1.0.4
[79] ggplot2_3.3.3 xfun_0.22
[81] ncdf4_1.17 tibble_3.1.0
[83] iterators_1.0.13 tinytex_0.30
[85] memoise_2.0.0 IRanges_2.24.1
[87] ellipsis_0.3.1 `

[jcapelladesto]

From this message of error in your installation:

Error: (converted from warning) package 'Rcpp' was built under R version 4.0.4 Execution halted ERROR: lazy loading failed for package 'geoRge'

I see you have R 4.0.3 installed. Try to execute the installation using R 4.0.4 or later. https://cran.r-project.org/bin/windows/base/ and then let me know if it runs