cmorris2945 commented 5 years ago

When I try to install this library, I keep getting this message in "R" language:

package ‘HuobinTan/scVAT’ is not available (for R version 3.5.1)

thbin commented 5 years ago

I have upgraded my R to version 3.5.1, and updated the package. Please retry it.

cmorris2945 commented 5 years ago

When I try to install this library: "rhdf5" I get this response:

Installing package into ‘C:/Users/chris/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) Warning message: package ‘rhdf5’ is not available (for R version 3.5.1)

Is there anyway else to install it??

cmorris2945 commented 5 years ago

Ok, that installation worked for thoselibraries. But when I try to install the devtools::install_github("HuobinTan/scVAT")

I get this message: devtools::install_github("HuobinTan/scVAT")

Downloading GitHub repo HuobinTan/scVAT@masterfrom URL https://api.github.com/repos/HuobinTan/scVAT/zipball/masterInstalling scVAT"C:/PROGRA~1/R/R-35~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD \ INSTALL \ "C:/Users/chris/AppData/Local/Temp/RtmpG0DMhB/devtools4e8c30942d2c/HuobinTan-scVAT-4085194" \ --library="C:/Users/chris/Documents/R/win-library/3.5" --install-tests

installing source package 'scVAT' ... R byte-compile and prepare package for lazy loadingWarning: replacing previous import 'igraph::groups' by 'plotly::groups' when loading 'scVAT'Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'DESeq2'ERROR: lazy loading failed for package 'scVAT'* removing 'C:/Users/chris/Documents/R/win-library/3.5/scVAT'In R CMD INSTALLInstallation failed: Command failed (1)

"Sports, football, beer and above all gambling, filled up the horizons of their minds. To keep people in control and ignorant was not difficult...."

George Orwell, author:'1984'

On Saturday, August 4, 2018, 9:13:39 PM EDT, Huobin Tan notifications@github.com wrote:

rhdf5 is from bioconductor not cran, please install it using commands as follows:

source("https://bioconductor.org/biocLite.R") biocLite("rhdf5")

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

thbin commented 5 years ago

Please install DESeq2 by bioconductor using commands as follows, same as rhdf5

source("https://bioconductor.org/biocLite.R") biocLite("DESeq2")

by the way, just rhdf5 and DESeq2 packages are from bioconductor, and installed using biocLite. all other packages are installed using install.packages.

cmorris2945 commented 5 years ago

stand by....

cmorris2945 commented 5 years ago

That seemed to work. Does this mean I have everything from: ("HuobinTan/scVAT") library installed??

cmorris2945 commented 5 years ago

This still does not let me install ("HuobinTan/scVAT") I have the same error as before: Warning message: package ‘HuobinTan/scVAT’ is not available (for R version 3.5.1)

thbin commented 5 years ago

This package is a source code from github, not cran package. So, you must install the package by devtools. the commands as follows:

install.package("devtools")
devtools::install_github("HuobinTan/scVAT")

cmorris2945 commented 5 years ago

I know, but installing it this way does not work though.

This is what I get when I install that:

Downloading GitHub repo HuobinTan/scVAT@master from URL https://api.github.com/repos/HuobinTan/scVAT/zipball/master Installing scVAT "C:/PROGRA~1/R/R-35~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD \ INSTALL \ "C:/Users/chris/AppData/Local/Temp/RtmpG0DMhB/devtools4e8c5e382626/HuobinTan-scVAT-4085194" \ --library="C:/Users/chris/Documents/R/win-library/3.5" --install-tests

installing source package 'scVAT' ... R byte-compile and prepare package for lazy loading Warning: replacing previous import 'igraph::groups' by 'plotly::groups' when loading 'scVAT' Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'stringi' ERROR: lazy loading failed for package 'scVAT'
removing 'C:/Users/chris/Documents/R/win-library/3.5/scVAT' In R CMD INSTALL Installation failed: Command failed (1)

cmorris2945 commented 5 years ago

I keep telling you....it does not work. I get that error message above....?

cmorris2945 commented 5 years ago

the devtools package installs, it's the other one there: devtools::install_github("HuobinTan/scVAT")- does not install....?

thbin commented 5 years ago

The error is "there is no package called 'stringi'", the shows you need install package 'stringi'. Please install the package using the command

install.packages("stringi")

By the way, scVAT needs the following pacakges:

  shiny
  shinydashboard
  plotly
  Matrix
  pbapply
  irlba
  Rtsne
  cccd
  igraph
  DT
  rhdf5
  DESeq2

Only two packages ('rhdf5', 'DESeq2') are from bioconductor, others are from CRAN. For bioconductor packages, please install them using the commands

source("https://bioconductor.org/biocLite.R")
biocLite("rhdf5")
biocLite("DESeq2")

For CRAN packages, please install them using install.packages:

install.packages("shiny")
install.packages("shinydashboard")
install.packages("plotly")
install.packages("Matrix")
install.packages("pbapply")
install.packages("irlba")
install.packages("Rtsne")
install.packages("cccd")
install.packages("igraph")
install.packages("DT")

cmorris2945 commented 5 years ago

standy by...

cmorris2945 commented 5 years ago

Ok, so I installed all of the CRAN packages.

But I still can't get the devtools::install_github("HuobinTan/scVAT")- to install

It gives me this error message when I install it now:

**ERROR: dependencies 'irlba', 'Rtsne', 'igraph' are not available for package 'scVAT'

removing 'C:/Users/chris/Documents/R/win-library/3.5/scVAT' In R CMD INSTALL Installation failed: Command failed (1)**

thbin commented 5 years ago

**ERROR: dependencies 'irlba', 'Rtsne', 'igraph' are not available for package 'scVAT' Please check the packages ready? If no, please install these packages: 'irlba', 'Rtsne', 'igraph'

install.packages("irlba")
install.packages("Rtsne")
install.packages("igraph")

cmorris2945 commented 5 years ago

I already installed those, but I'll do it again, hold on....

cmorris2945 commented 5 years ago

they're all installed this is what it said:

install.packages("Rtsne") Installing package into ‘C:/Users/chris/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://mirrors.sorengard.com/cran/bin/windows/contrib/3.5/Rtsne_0.13.zip' Content type 'application/zip' length 616113 bytes (601 KB) downloaded 601 KB

package ‘Rtsne’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘Rtsne’

The downloaded binary packages are in C:\Users\chris\AppData\Local\Temp\RtmpG0DMhB\downloaded_packages

install.packages("igraph") Installing package into ‘C:/Users/chris/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://mirrors.sorengard.com/cran/bin/windows/contrib/3.5/igraph_1.2.2.zip' Content type 'application/zip' length 9149416 bytes (8.7 MB) downloaded 8.7 MB

package ‘igraph’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘igraph’

The downloaded binary packages are in C:\Users\chris\AppData\Local\Temp\RtmpG0DMhB\downloaded_packages

devtools::install_github("HuobinTan/scVAT") Downloading GitHub repo HuobinTan/scVAT@master from URL https://api.github.com/repos/HuobinTan/scVAT/zipball/master Installing scVAT Installing 1 package: igraph Installing package into ‘C:/Users/chris/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://mirrors.sorengard.com/cran/bin/windows/contrib/3.5/igraph_1.2.2.zip' Content type 'application/zip' length 9149416 bytes (8.7 MB) downloaded 8.7 MB

package ‘igraph’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘igraph’

The downloaded binary packages are in C:\Users\chris\AppData\Local\Temp\RtmpG0DMhB\downloaded_packages

cmorris2945 commented 5 years ago

But I still can't install the: devtools::install_github("HuobinTan/scVAT")

thbin commented 5 years ago

Maybe you try load the packages, check them ready? For example, you may use the command, then check the log is ok?

library(Rtsne)

In addition, you may try to run your R as Administrator.

cmorris2945 commented 5 years ago

Error in library(Rtsne) : there is no package called ‘Rtsne’

cmorris2945 commented 5 years ago

I'll try to run as an administrator. (didn't know you could do that.)

cmorris2945 commented 5 years ago

does it matter where the "CRAN" mirror is?? I pick USA(NY)[https]

cmorris2945 commented 5 years ago

I think it's in now. When I run the library(scVAT) I get this:

library(scVAT) Warning messages: 1: replacing previous import ‘igraph::groups’ by ‘plotly::groups’ when loading ‘scVAT’ 2: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘scVAT’ 3: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘scVAT’

cmorris2945 commented 5 years ago

This means it is installed correct??

devtools::install_github("HuobinTan/scVAT") Downloading GitHub repo HuobinTan/scVAT@master from URL https://api.github.com/repos/HuobinTan/scVAT/zipball/master Installing scVAT "C:/PROGRA~1/R/R-35~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD \ INSTALL \ "C:/Users/chris/AppData/Local/Temp/RtmpkJ0Ugy/devtools1d04172c1f9d/HuobinTan-scVAT-4085194" \ --library="C:/Users/chris/Documents/R/win-library/3.5" --install-tests

installing source package 'scVAT' ... R byte-compile and prepare package for lazy loading Warning: replacing previous import 'igraph::groups' by 'plotly::groups' when loading 'scVAT' Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'scVAT' Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'scVAT' Note: ... may be used in an incorrect context help * installing help indices converting help for package 'scVAT' finding HTML links ... done VATEntity html
addCellProp html
addGeneProp html
addPropMeta html
buildKNNGraph html
clusterGraph html
doAllDiffAnalysis html
doCluster html
doDESeq2Test html
doDiffAnalysis html
doPCA html
doTSNE html
doTTest html
doWilcoxTest html
filterCells html
filterGenes html
getAnalysisColName html
getAnalysisColnames html
getAnalysisData html
getAnalysisKey html
getAnalysisList html
getCellPropData html
getGenePropData html
getPropMeta html
getUseData html
initVATEntity html
load10XH5 html
load10XPath html
loadAnalysis html
loadAnalysisFromCSV html
loadCSVData html
plotAnalysis html
plotGene html
plotGenes html
plotPC html
plotPCASDev html
plotTSNE html
plotThreeGenes html
plotTwoGenes html
saveVATToCSV html
setGenePercent html
show-methods html
startVATGUI html
building package indices * testing if installed package can be loaded arch - i386 Warning: replacing previous import 'igraph::groups' by 'plotly::groups' when loading 'scVAT' Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'scVAT' Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'scVAT' *** arch - x64 Warning: replacing previous import 'igraph::groups' by 'plotly::groups' when loading 'scVAT' Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'scVAT' Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'scVAT'
DONE (scVAT) In R CMD INSTALL

thbin commented 5 years ago

Congratulations, It's OK! You may follow the docs/vignette.html to try the package.

cmorris2945 commented 5 years ago

Thank you! You're the best!

I'm probably going to need some more help when it comes to analyzing this cell data. I have a dataset of 7000 cells, and about 30000 genes.

I'm going to try and follow this single-cell RNA Visual Analysis Toolkit. But I'll probably get stuck....

HuobinTan / scVAT

package ‘HuobinTan/scVAT’ is not available (for R version 3.5.1) #2

rhdf5 is from bioconductor not cran, please install it using commands as follows:

Please install DESeq2 by bioconductor using commands as follows, same as rhdf5

by the way, just rhdf5 and DESeq2 packages are from bioconductor, and installed using biocLite. all other packages are installed using install.packages.