issues when installing ITALK

[xinmiaoyan]

hi, I used the code to install iTALK nd tried many time but failed, would you help? thanks so much

the code: devtools::install_github("Coolgenome/iTALK", build_vignettes = TRUE, force = TRUE)

the bug: `Downloading GitHub repo Coolgenome/iTALK@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: slam (0.1-48 -> 0.1-49) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 slam (0.1-48 -> 0.1-49) [CRAN] Installing 1 packages: slam

There is a binary version available but the source version is later: binary source needs_compilation slam 0.1-48 0.1-49 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) n trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/slam_0.1-48.tgz' Content type 'application/x-gzip' length 202614 bytes (197 KB)

downloaded 197 KB

The downloaded binary packages are in /var/folders/vg/bnpr7f252gvg68_50qt12_z9dxfpv0/T//RtmpsCskTx/downloaded_packages ✓ checking for file ‘/private/var/folders/vg/bnpr7f252gvg68_50qt12_z9dxfpv0/T/RtmpsCskTx/remotes9dfd4e974e05/Coolgenome-iTALK-6d9b390/DESCRIPTION’ ... ─ preparing ‘iTALK’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories NB: this package now depends on R (>= 3.5.0) WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘iTALK/R/sysdata.rda’ ‘iTALK/data/LR_database.rda’ ─ building ‘iTALK_0.1.0.tar.gz’ Warning in sprintf(gettext(fmt, domain = domain), ...) : one argument not used by format 'invalid uid value replaced by that for user 'nobody'' Warning: invalid uid value replaced by that for user 'nobody' Warning in sprintf(gettext(fmt, domain = domain), ...) : one argument not used by format 'invalid gid value replaced by that for user 'nobody'' Warning: invalid gid value replaced by that for user 'nobody'

• installing source package ‘iTALK’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘iTALK’ Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::%s%’ by ‘network::%s%’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::add.edges’ by ‘network::add.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.edge.attribute’ by ‘network::get.edge.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::add.vertices’ by ‘network::add.vertices’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::%c%’ by ‘network::%c%’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::list.vertex.attributes’ by ‘network::list.vertex.attributes’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::set.edge.attribute’ by ‘network::set.edge.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::is.directed’ by ‘network::is.directed’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::set.vertex.attribute’ by ‘network::set.vertex.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.vertex.attribute’ by ‘network::get.vertex.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::delete.edges’ by ‘network::delete.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::is.bipartite’ by ‘network::is.bipartite’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.edges’ by ‘network::get.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::list.edge.attributes’ by ‘network::list.edge.attributes’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::delete.vertices’ by ‘network::delete.vertices’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::crossing’ by ‘tidyr::crossing’ when loading ‘iTALK’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘iTALK’ Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::%s%’ by ‘network::%s%’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::add.edges’ by ‘network::add.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.edge.attribute’ by ‘network::get.edge.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::add.vertices’ by ‘network::add.vertices’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::%c%’ by ‘network::%c%’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::list.vertex.attributes’ by ‘network::list.vertex.attributes’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::set.edge.attribute’ by ‘network::set.edge.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::is.directed’ by ‘network::is.directed’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::set.vertex.attribute’ by ‘network::set.vertex.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.vertex.attribute’ by ‘network::get.vertex.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::delete.edges’ by ‘network::delete.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::is.bipartite’ by ‘network::is.bipartite’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.edges’ by ‘network::get.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::list.edge.attributes’ by ‘network::list.edge.attributes’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::delete.vertices’ by ‘network::delete.vertices’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::crossing’ by ‘tidyr::crossing’ when loading ‘iTALK’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::union’ by ‘igraph::union’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::as_data_frame’ by ‘igraph::as_data_frame’ when loading ‘iTALK’ Warning: replacing previous import ‘circlize::degree’ by ‘igraph::degree’ when loading ‘iTALK’ Warning: replacing previous import ‘dplyr::groups’ by ‘igraph::groups’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::%s%’ by ‘network::%s%’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::add.edges’ by ‘network::add.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.edge.attribute’ by ‘network::get.edge.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::add.vertices’ by ‘network::add.vertices’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::%c%’ by ‘network::%c%’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::list.vertex.attributes’ by ‘network::list.vertex.attributes’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::set.edge.attribute’ by ‘network::set.edge.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::is.directed’ by ‘network::is.directed’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::set.vertex.attribute’ by ‘network::set.vertex.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.vertex.attribute’ by ‘network::get.vertex.attribute’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::delete.edges’ by ‘network::delete.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::is.bipartite’ by ‘network::is.bipartite’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::get.edges’ by ‘network::get.edges’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::list.edge.attributes’ by ‘network::list.edge.attributes’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::delete.vertices’ by ‘network::delete.vertices’ when loading ‘iTALK’ Warning: replacing previous import ‘igraph::crossing’ by ‘tidyr::crossing’ when loading ‘iTALK’ ** testing if installed package keeps a record of temporary installation path
• DONE (iTALK)

library(iTALK) Error: package or namespace load failed for ‘iTALK’ in get(method, envir = home): lazy-load database '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/coin/R/coin.rdb' is corrupt In addition: There were 23 warnings (use warnings() to see them)`

[kathy1234WU]

Hi,

I just installed iTALK with the following code Not sure if it helps you

library(devtools) install_github("Coolgenome/iTALK", build_vignettes = TRUE) install.packages("ps") install.packages("scater") BiocManager::install("scater")

devtools::install_github('arc85/celltalker') install.packages("G://google Downloads/iTALK-master/",repos=NULL,type="source")

######################### library(iTALK) library(Seurat) library(Matrix) library(dplyr) library(igraph)

Depending on your computer, there may be some packages that need to be installed first

Good luck!