Closed EmilyHoedt closed 3 years ago
adw96
commented
3 years ago Hi @EmilyHoedt -- could you please provide your R version and session info? An example of how to do so is here: adw96/breakaway#79
I expect that the issue is that you have not yet installed phyloseq
Cheers,
Amy
EmilyHoedt
commented
3 years ago Hi Amy, Thanks very much for your reply. I had installed phyloseq and breakaway, but still ran into problems with DivNet. I've added the details for my R version and session below. Thanks again
library(breakaway) library(phyloseq) Warning message: package ‘phyloseq’ was built under R version 4.0.3 library(magrittr) Warning message: package ‘magrittr’ was built under R version 4.0.3 library(tidyverse) -- Attaching packages -------------------------------------------------------------------------------- tidyverse 1.3.0 -- v ggplot2 3.3.3.9000 v purrr 0.3.4
v tibble 3.0.5 v dplyr 1.0.3
v tidyr 1.1.2 v stringr 1.4.0
v readr 1.4.0 v forcats 0.5.0
-- Conflicts ----------------------------------------------------------------------------------- tidyverse_conflicts() -- x tidyr::extract() masks magrittr::extract() x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag() x purrr::set_names() masks magrittr::setnames() Warning messages: 1: package ‘tidyverse’ was built under R version 4.0.3 2: package ‘tidyr’ was built under R version 4.0.3 3: package ‘readr’ was built under R version 4.0.3 4: package ‘purrr’ was built under R version 4.0.3 5: package ‘stringr’ was built under R version 4.0.3 6: package ‘forcats’ was built under R version 4.0.3 R.version
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 4
minor 0.2
year 2020
month 06
day 22
svn rev 78730
language R
version.string R version 4.0.2 (2020-06-22) nickname Taking Off Again
sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.3 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[7] tibble_3.0.5 ggplot2_3.3.3.9000 tidyverse_1.3.0 magrittr_2.0.1 phyloseq_1.34.0 breakaway_4.7.3
loaded via a namespace (and not attached):
[1] nlme_3.1-151 fs_1.5.0 matrixStats_0.57.0 lubridate_1.7.9.2 RColorBrewer_1.1-2
[6] progress_1.2.2 httr_1.4.2 tools_4.0.2 backports_1.2.1 R6_2.5.0
[11] vegan_2.5-7 DBI_1.1.1 BiocGenerics_0.36.0 mgcv_1.8-33 colorspace_2.0-0
[16] permute_0.9-5 rhdf5filters_1.2.0 ade4_1.7-16 withr_2.4.0 tidyselect_1.1.0
[21] gridExtra_2.3 prettyunits_1.1.1 compiler_4.0.2 cli_2.2.0 rvest_0.3.6
[26] Biobase_2.50.0 xml2_1.3.2 scales_1.1.1 minqa_1.2.4 XVector_0.30.0
[31] pkgconfig_2.0.3 lme4_1.1-26 dbplyr_2.0.0 rlang_0.4.10 readxl_1.3.1
[36] rstudioapi_0.13 generics_0.1.0 jsonlite_1.7.2 biomformat_1.7.0 Matrix_1.2-18
[41] fansi_0.4.2 Rcpp_1.0.6 munsell_0.5.0 S4Vectors_0.28.1 Rhdf5lib_1.12.0
[46] ape_5.4-1 lifecycle_0.2.0 stringi_1.5.3 MASS_7.3-53 zlibbioc_1.36.0
[51] rhdf5_2.34.0 plyr_1.8.6 grid_4.0.2 parallel_4.0.2 ggrepel_0.9.1
[56] crayon_1.3.4 lattice_0.20-41 Biostrings_2.58.0 haven_2.3.1 splines_4.0.2
[61] multtest_2.46.0 hms_1.0.0 pillar_1.4.7 igraph_1.2.6 boot_1.3-25
[66] corpcor_1.6.9 reshape2_1.4.4 codetools_0.2-18 mixOmics_6.14.0 stats4_4.0.2
[71] reprex_0.3.0 glue_1.4.2 data.table_1.13.6 modelr_0.1.8 vctrs_0.3.6
[76] nloptr_1.2.2.2 foreach_1.5.1 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[81] xfun_0.20 broom_0.7.3 RSpectra_0.16-0 survival_3.2-7 rARPACK_0.11-0
[86] iterators_1.0.13 tinytex_0.29 IRanges_2.24.1 ellipse_0.4.2 cluster_2.1.0
[91] statmod_1.4.35 ellipsis_0.3.1
EmilyHoedt
commented
3 years ago I fixed the issue. I replaced R and R studio with the latest version (R v4.0.3). I then had in issue with tidyr not being recognized in the architecture. Although it was uninstalled the folder was still present with the R/win-library so the reinstallation of tidyr wasn't working. The folder couldn't be deleted, so I renamed it and from there tidyr and DivNet installation all worked smoothly.
I wanted to share the information here in case anyone else struggles in future.
Thank you!
adw96
commented
3 years ago Thanks @EmilyHoedt for figuring this out and posting!
Hello I have installed breakaway, but when I try to install DivNet I get the following error. A similar error occurred when I tried to install ampvis2 previously and fixed it by
devtools::install_github("tidyverse/ggplot2")Any suggestions for successful DivNet install would be greatly appreciated. Thank you, Emily`> remotes::install_github("adw96/DivNet") Downloading GitHub repo adw96/DivNet@HEAD Skipping 1 packages not available: phyloseq √ checking for file 'C:\Users\ech132\AppData\Local\Temp\1\RtmpWgjvz0\remotes617014cd2c52\adw96-DivNet-31e04e2/DESCRIPTION' (394ms)
preparing 'DivNet': √ checking DESCRIPTION meta-information ...
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories
building 'DivNet_0.3.6.tar.gz'
installing source package 'DivNet' ... using staged installation R ** data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading Error: (converted from warning) package 'phyloseq' was built under R version 4.0.3 Execution halted ERROR: lazy loading failed for package 'DivNet'
removing 'C:/Program Files/R/R-4.0.2/library/DivNet' Error: Failed to install 'DivNet' from GitHub: (converted from warning) installation of package ‘C:/Users/ech132/AppData/Local/Temp/1/RtmpWgjvz0/file61703f094f39/DivNet_0.3.6.tar.gz’ had non-zero exit status`