Problem installing vmikk/metagMisc

avportal commented 4 years ago

Hi there,

I am trying to install vmikk/metagMisc as follows:

devtools::install_github("vmikk/metagMisc")

However, I get the following error:

Downloading GitHub repo vmikk/metagMisc@master Skipping 1 packages not available: phyloseq ✓ checking for file ‘/private/var/folders/st/y2p98lbd0y58731wvyg2rgpc0000gp/T/Rtmp2soaSi/remotese111f52b72d/vmikk-metagMisc-d25b92f/DESCRIPTION’ (338ms) ─ preparing ‘metagMisc’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘metagMisc_0.0.4.tar.gz’

installing source package ‘metagMisc’ ... using staged installation R ** byte-compile and prepare package for lazy loading Error in phy_tree(physeq, errorIfNULL = F) : could not find function "phy_tree" Error: unable to load R code in package ‘metagMisc’ Execution halted ERROR: lazy loading failed for package ‘metagMisc’
removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/metagMisc’ Error: Failed to install 'metagMisc' from GitHub: (converted from warning) installation of package ‘/var/folders/st/y2p98lbd0y58731wvyg2rgpc0000gp/T//Rtmp2soaSi/filee116f77fb6b/metagMisc_0.0.4.tar.gz’ had non-zero exit status

Any help will be appreciated

Session information: R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] remotes_2.1.1 phyloseq_1.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.4 ape_5.3 lattice_0.20-38
[4] prettyunits_1.1.1 ps_1.3.2 Biostrings_2.54.0
[7] assertthat_0.2.1 rprojroot_1.3-2 digest_0.6.25
[10] foreach_1.4.8 R6_2.4.1 plyr_1.8.6
[13] backports_1.1.5 stats4_3.6.2 ggplot2_3.3.0
[16] pillar_1.4.3 zlibbioc_1.32.0 rlang_0.4.5
[19] curl_4.3 rstudioapi_0.11 data.table_1.12.8
[22] vegan_2.5-6 callr_3.4.2 S4Vectors_0.24.3
[25] Matrix_1.2-18 desc_1.2.0 devtools_2.2.2
[28] splines_3.6.2 stringr_1.4.0 igraph_1.2.4.2
[31] munsell_0.5.0 compiler_3.6.2 pkgconfig_2.0.3
[34] BiocGenerics_0.32.0 multtest_2.42.0 pkgbuild_1.0.6
[37] mgcv_1.8-31 biomformat_1.14.0 tidyselect_1.0.0
[40] tibble_2.1.3 IRanges_2.20.2 codetools_0.2-16
[43] fansi_0.4.1 permute_0.9-5 crayon_1.3.4
[46] dplyr_0.8.5 withr_2.1.2 MASS_7.3-51.4
[49] grid_3.6.2 nlme_3.1-142 jsonlite_1.6.1
[52] gtable_0.3.0 lifecycle_0.2.0 magrittr_1.5
[55] scales_1.1.0 cli_2.0.2 stringi_1.4.6
[58] XVector_0.26.0 reshape2_1.4.3 fs_1.3.1
[61] testthat_2.3.2 ellipsis_0.3.0 Rhdf5lib_1.8.0
[64] iterators_1.0.12 tools_3.6.2 ade4_1.7-13
[67] Biobase_2.46.0 glue_1.3.2 purrr_0.3.3
[70] pkgload_1.0.2 processx_3.4.2 parallel_3.6.2
[73] survival_3.1-8 colorspace_1.4-1 rhdf5_2.30.1
[76] cluster_2.1.0 sessioninfo_1.1.1 memoise_1.1.0
[79] usethis_1.5.1

vmikk commented 4 years ago

Hello @avportal ! Thank you for pointing out this bug, it is fixed now. Please re-install the package and let me know if it works for you now.

With best regards, Vladimir

avportal commented 4 years ago

Hi Vladimir,

Thanks a lot for your help.

The installation worked, but now I am getting a new error message:

library(vmikk/metagMisc) Error in library(vmikk/metagMisc) : 'package' must be of length 1

Cheers,

Angel

sessionInfo()

R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.3

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale: [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods
[7] base

other attached packages: [1] phyloseq_1.30.0

loaded via a namespace (and not attached): [1] remotes_2.1.1 reshape2_1.4.3 splines_3.6.3
[4] lattice_0.20-40 rhdf5_2.30.1 colorspace_1.4-1
[7] stats4_3.6.3 mgcv_1.8-31 survival_3.1-11
[10] rlang_0.4.5 pkgbuild_1.0.6 pillar_1.4.3
[13] withr_2.1.2 glue_1.3.2 BiocGenerics_0.32.0 [16] foreach_1.4.8 lifecycle_0.2.0 plyr_1.8.6
[19] stringr_1.4.0 zlibbioc_1.32.0 Biostrings_2.54.0
[22] munsell_0.5.0 gtable_0.3.0 codetools_0.2-16
[25] Biobase_2.46.0 permute_0.9-5 callr_3.4.2
[28] IRanges_2.20.2 ps_1.3.2 biomformat_1.14.0
[31] parallel_3.6.3 fansi_0.4.1 Rcpp_1.0.4
[34] backports_1.1.5 scales_1.1.0 BiocManager_1.30.10 [37] vegan_2.5-6 S4Vectors_0.24.3 jsonlite_1.6.1
[40] XVector_0.26.0 ggplot2_3.3.0 stringi_1.4.6
[43] processx_3.4.2 grid_3.6.3 ade4_1.7-15
[46] rprojroot_1.3-2 cli_2.0.2 tools_3.6.3
[49] magrittr_1.5 tibble_2.1.3 cluster_2.1.0
[52] crayon_1.3.4 ape_5.3 pkgconfig_2.0.3
[55] MASS_7.3-51.5 Matrix_1.2-18 data.table_1.12.8
[58] prettyunits_1.1.1 assertthat_0.2.1 rstudioapi_0.11
[61] iterators_1.0.12 Rhdf5lib_1.8.0 R6_2.4.1
[64] multtest_2.42.0 igraph_1.2.5 nlme_3.1-145
[67] compiler_3.6.3

vmikk commented 4 years ago

Hello Angel,

Loading the package with library(metagMisc) should work (you don't need to add "vmikk" there).

With best regards, Vladimir

avportal commented 4 years ago

Thanks Vladimir.

It worked.

Cheers, Angel

vmikk commented 4 years ago

Fixed with 2502dfe0f75060405fefe11726841367f509e7f8.

vmikk / metagMisc

Problem installing vmikk/metagMisc #14