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kimpenn / PIVOT

Platform for Interactive analysis and Visualization Of Transcriptomics data
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Failed to install 'PIVOT' from GitHub #16

Closed annaeoc closed 4 years ago

annaeoc commented 4 years ago

I have R studio 3.6.3 and I cannot install PIVOT I run:

install.packages('tidyr') library(Seurat) install.packages("devtools") library("devtools") library(tidyr) BiocManager::install( ) devtools::install_github("tidyverse/tidyr") install.packages("remotes") install_github("qinzhu/PIVOT")

or

install_github("qinzhu/PIVOT ", force=TRUE)

but I get : Failed to install 'PIVOT' from GitHub

eturkes commented 4 years ago

There's probably a dependency issue, i.e. you need to compile a package but the appropriate header files are not installed. Can you run install_github("qinzhu/PIVOT") again and post the entire output past that line?

annaeoc commented 4 years ago

Error in install_github("qinzhu/PIVOT ", force = TRUE) : can not find the function "install_github"

qinzhu commented 4 years ago

Please run library("devtools") before calling install_github("qinzhu/PIVOT ", force = TRUE)

annaeoc commented 4 years ago

Sorry but I get this:

library("devtools") install_github("qinzhu/PIVOT ", force = TRUE) Errore: Failed to install 'unknown package' from GitHub: JSON: EXPECTED value GOT <

Da: Qin Zhu notifications@github.com Inviato: mercoledì, 15. aprile 2020 13:32:02 A: qinzhu/PIVOT Cc: Rinaldi Anna; Author Oggetto: Re: [qinzhu/PIVOT] Failed to install 'PIVOT' from GitHub (#16)

Please run library("devtools") before calling install_github("qinzhu/PIVOT ", force = TRUE)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/qinzhu/PIVOT/issues/16#issuecomment-614042590, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APDMY4QUDK7LUF2NLMO2EL3RMWZNFANCNFSM4MERJVNA.

eturkes commented 4 years ago

It sounds to me like you're getting a new error now. I'd try running install_github("qinzhu/PIVOT ", force = TRUE) every now and then and see if it resolves that issue on its own. If it does, and you start getting a different kind of error, please post the output of that.

In the meanwhile, can you do library("devtools") and then copy paste the output of sessionInfo() here?

annaeoc commented 4 years ago

Session info:

R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LC_COLLATE=Italian_Switzerland.1252 LC_CTYPE=Italian_Switzerland.1252 LC_MONETARY=Italian_Switzerland.1252 [4] LC_NUMERIC=C LC_TIME=Italian_Switzerland.1252

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

other attached packages: [1] devtools_2.2.2 usethis_1.5.1 Seurat_3.1.4

loaded via a namespace (and not attached): [1] TH.data_1.0-10 Rtsne_0.15 colorspace_1.4-1 ellipsis_0.3.0 ggridges_0.5.2 rprojroot_1.3-2
[7] fs_1.4.0 rstudioapi_0.11 leiden_0.3.3 listenv_0.8.0 npsurv_0.4-0 remotes_2.1.1
[13] ggrepel_0.8.1 fansi_0.4.1 mvtnorm_1.1-0 codetools_0.2-16 splines_3.6.3 mnormt_1.5-6
[19] lsei_1.2-0 TFisher_0.2.0 pkgload_1.0.2 jsonlite_1.6.1 ica_1.0-2 cluster_2.1.0
[25] png_0.1-7 uwot_0.1.5 sctransform_0.2.1 compiler_3.6.3 httr_1.4.1 backports_1.1.5
[31] assertthat_0.2.1 Matrix_1.2-18 lazyeval_0.2.2 cli_2.0.2 prettyunits_1.1.1 htmltools_0.4.0
[37] tools_3.6.3 rsvd_1.0.3 igraph_1.2.5 gtable_0.3.0 glue_1.3.1 RANN_2.6.1
[43] reshape2_1.4.3 dplyr_0.8.4 rappdirs_0.3.1 Rcpp_1.0.3 Biobase_2.46.0 vctrs_0.2.3
[49] multtest_2.42.0 gdata_2.18.0 ape_5.3 nlme_3.1-144 gbRd_0.4-11 lmtest_0.9-37
[55] stringr_1.4.0 ps_1.3.2 globals_0.12.5 testthat_2.3.2 lifecycle_0.2.0 irlba_2.3.3
[61] gtools_3.8.1 future_1.16.0 MASS_7.3-51.5 zoo_1.8-7 scales_1.1.0 parallel_3.6.3
[67] sandwich_2.5-1 RColorBrewer_1.1-2 curl_4.3 memoise_1.1.0 reticulate_1.14 pbapply_1.4-2
[73] gridExtra_2.3 ggplot2_3.2.1 stringi_1.4.6 desc_1.2.0 mutoss_0.1-12 plotrix_3.7-7
[79] caTools_1.18.0 BiocGenerics_0.32.0 pkgbuild_1.0.6 bibtex_0.4.2.2 Rdpack_0.11-1 rlang_0.4.4
[85] pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-38 ROCR_1.0-7 purrr_0.3.3 patchwork_1.0.0
[91] htmlwidgets_1.5.1 processx_3.4.2 cowplot_1.0.0 tidyselect_1.0.0 RcppAnnoy_0.0.15 plyr_1.8.5
[97] magrittr_1.5 R6_2.4.1 gplots_3.0.3 multcomp_1.4-13 withr_2.1.2 pillar_1.4.3
[103] sn_1.6-1 fitdistrplus_1.0-14 survival_3.1-8 tibble_2.1.3 future.apply_1.4.0 tsne_0.1-3
[109] crayon_1.3.4 KernSmooth_2.23-16 plotly_4.9.2.1 grid_3.6.3 data.table_1.12.8 callr_3.4.3
[115] metap_1.3 digest_0.6.25 tidyr_1.0.2 numDeriv_2016.8-1.1 RcppParallel_4.4.4 stats4_3.6.3
[121] munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1

annaeoc commented 4 years ago

I get this warning after installing Seurat, can be a problem?

Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\multtest\libs\x64\multtest.dll to C:\Users\Utente\Documents\R\win-library\3.6\multtest\libs\x64\multtest.dll: Permission denied 2: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\dplyr\libs\x64\dplyr.dll to C:\Users\Utente\Documents\R\win-library\3.6\dplyr\libs\x64\dplyr.dll: Permission denied 3: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\glue\libs\x64\glue.dll to C:\Users\Utente\Documents\R\win-library\3.6\glue\libs\x64\glue.dll: Permission denied 4: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\gtools\libs\x64\gtools.dll to C:\Users\Utente\Documents\R\win-library\3.6\gtools\libs\x64\gtools.dll: Permission denied 5: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\Rcpp\libs\x64\Rcpp.dll to C:\Users\Utente\Documents\R\win-library\3.6\Rcpp\libs\x64\Rcpp.dll: Permission denied 6: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\RcppAnnoy\libs\x64\RcppAnnoy.dll to C:\Users\Utente\Documents\R\win-library\3.6\RcppAnnoy\libs\x64\RcppAnnoy.dll: Permission denied 7: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\Utente\Documents\R\win-library\3.6\rlang\libs\x64\rlang.dll: Permission denied 8: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\Utente\Documents\R\win-library\3.6\00LOCK\tibble\libs\x64\tibble.dll to C:\Users\Utente\Documents\R\win-library\3.6\tibble\libs\x64\tibble.dll: Permission denied

annaeoc commented 4 years ago

And this error running library (Seurat)

Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace ‘rlang’ 0.4.4 is already loaded, but >= 0.4.5 is required

annaeoc commented 4 years ago

I finally maded it: with Rstudio 3.6 you must install PIVOT by this command

BiocManager::install_github("qinzhu/PIVOT ", force = TRUE)

Install seurat

install.packages('BiocManager') BiocManager::install('multtest') install.packages('Seurat') library(Seurat)

update all

Install monocle

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("monocle")

install.packages("usethis") library("usethis") library("devtools") library('Seurat')

Install PIVOT

BiocManager::install_github("qinzhu/PIVOT ", force = TRUE) library(PIVOT) pivot()

eturkes commented 4 years ago

Not an expert on this but looking through those errors it seems there were issues with Windows trying to modify files currently in use. I'm not entirely sure using install_github from BiocManager was the solution or a just a coincidence... nonetheless happy you got it installed in the end!