rachaelantwis commented 7 years ago

Hi, sorry to post with so many issues. I'm new to R and microbiome data processing. I'm now having problems installing shiny-phyloseq. This is the error message:

shiny::runGitHub("shiny-phyloseq","joey711") Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz Loading required package: shiny Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help The following package is missing. shinythemes Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

Please can you help? Many thanks

spholmes commented 7 years ago

Maybe install shinythemes first by hand by typing and retry

install.packages("shinythemes")

On Mon, Jul 24, 2017 at 2:34 AM, rachaelantwis notifications@github.com wrote:

Hi, sorry to post with so many issues. I'm new to R and microbiome processing. I'm now having problems installing shiny-phyloseq. This is the error message:

shiny::runGitHub("shiny-phyloseq","joey711") Downloading https://github.com/joey711/shiny-phyloseq/archive/master. tar.gz Loading required package: shiny Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help The following package is missing. shinythemes Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

Please can you help? Many thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/74, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvf4i0CodykQLYM3SCYia69XO_gwvks5sRGU4gaJpZM4Og8VG .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

rachaelantwis commented 7 years ago

This hasn’t seemed to fix it. I’m not sure where the object “i” originates? Thank you

On 24 Jul 2017, at 16:03, Susan Holmes notifications@github.com wrote:

Maybe install shinythemes first by hand by typing and retry

install.packages("shinythemes")

On Mon, Jul 24, 2017 at 2:34 AM, rachaelantwis notifications@github.com wrote:

Hi, sorry to post with so many issues. I'm new to R and microbiome processing. I'm now having problems installing shiny-phyloseq. This is the error message:

shiny::runGitHub("shiny-phyloseq","joey711") Downloading https://github.com/joey711/shiny-phyloseq/archive/master. tar.gz Loading required package: shiny Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help The following package is missing. shinythemes Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

Please can you help? Many thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/74, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvf4i0CodykQLYM3SCYia69XO_gwvks5sRGU4gaJpZM4Og8VG .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/74#issuecomment-317451829, or mute the thread https://github.com/notifications/unsubscribe-auth/AcwXLVE7jPphFSWA2dcXmhvbmqJxkcwOks5sRLIzgaJpZM4Og8VG.

spholmes commented 7 years ago

Rachael, I believe you have found a bug in the install when I replace the i in the function with pkg everything works.

See the manual install section here: http://joey711.github.io/shiny-phyloseq/Install.html

you will see there is an install.R file you can download it and tailor it or run through it line by line to check what is not working on your machine. Edit the end of the function install_missing_packages to make i into pkg as follows:

devtools::source_url("https://raw.githubusercontent.com/joey711/shiny-phyloseq/master/install.R")

https://raw.githubusercontent.com/joey711/shiny-phyloseq/master/install.R

deppkgs = c(phyloseq = "1.16.0", biomformat = "1.0.0", shiny = "0.13.2", shinythemes = "1.0.1", ggplot2 = "2.1.0", data.table = "1.9.6", networkD3 = "0.2.10", genefilter = "1.54.0", grid = "3.3.0", gridExtra = "2.2.1", markdown = "0.7.7", rmarkdown = "0.9.6", png = "0.1.7", RColorBrewer = "1.1.2", scales = "0.4.0")

install_missing_packages = function(pkg, version = NULL, verbose = TRUE){ availpacks = .packages(all.available = TRUE) source("http://bioconductor.org/biocLite.R") missingPackage = FALSE if(!any(pkg %in% availpacks)){ if(verbose){ message("The following package is missing.\n", pkg, "\n", "Installation will be attempted...") } missingPackage <- TRUE } if(!is.null(version) & !missingPackage){

version provided and package not missing, so compare.

if( compareVersion(a = as.character(packageVersion(pkg)),
                   b = version) < 0 ){
  if(verbose){
    message("Current version of package\n",
            pkg, "\t",
            packageVersion(pkg), "\n",
            "is less than required.
            Update will be attempted.")
  }
  missingPackage <- TRUE
  }

} if(missingPackage){ biocLite(pkg, suppressUpdates = TRUE) } }

pkg1 = mapply(install_missing_packages, pkg = names(deppkgs),

version = deppkgs,

          MoreArgs = list(verbose = TRUE),
          SIMPLIFY = FALSE,
          USE.NAMES = TRUE)

On Mon, Jul 24, 2017 at 11:01 AM, rachaelantwis notifications@github.com wrote:

This hasn’t seemed to fix it. I’m not sure where the object “i” originates? Thank you

On 24 Jul 2017, at 16:03, Susan Holmes notifications@github.com wrote:

Maybe install shinythemes first by hand by typing and retry

install.packages("shinythemes")

On Mon, Jul 24, 2017 at 2:34 AM, rachaelantwis <notifications@github.com

wrote:

Hi, sorry to post with so many issues. I'm new to R and microbiome processing. I'm now having problems installing shiny-phyloseq. This is the error message:

shiny::runGitHub("shiny-phyloseq","joey711") Downloading https://github.com/joey711/shiny-phyloseq/archive/master. tar.gz Loading required package: shiny Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help The following package is missing. shinythemes Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

Please can you help? Many thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/74, or mute the thread https://github.com/notifications/unsubscribe-auth/ ABJcvf4i0CodykQLYM3SCYia69XO_gwvks5sRGU4gaJpZM4Og8VG .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/joey711/shiny-phyloseq/issues/74#issuecomment-317451829>, or mute the thread https://github.com/notifications/unsubscribe-auth/ AcwXLVE7jPphFSWA2dcXmhvbmqJxkcwOks5sRLIzgaJpZM4Og8VG.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/74#issuecomment-317505088, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvRLFiABlhRxeoovencKQNMapQpigks5sRNvngaJpZM4Og8VG .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

spholmes commented 7 years ago

We will fix this shortly but let us know if that workaround is OK for you? @joey711? Have you seen this?

rachaelantwis commented 7 years ago

Thanks very much for this, it's working now!

joey711 commented 7 years ago

Thanks for posting. We'll put in the fix soon so others may benefit.

2533245542 commented 7 years ago

This problem hasnt been resolved. Can you please update the text in the following URL?https://raw.githubusercontent.com/joey711/shiny-phyloseq/master/install.R

foamy1881 commented 7 years ago

The problem still persist. Can someone please look at this?

Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz Loading required package: shiny Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help The following package is missing. phyloseq Installation will be attempted... Error in "BiocUpgrade" %in% pkgs : object 'i' not found

Maddocent commented 7 years ago

I have the same problem, Error in "BiocUpgrade" %in% pkgs : object 'i' not found. Running R on RStudio Server Open Source on Ubuntu.

Maddocent commented 7 years ago

Instead of using your convoluted for loop I've replaced the loop for a call to lapply. Generate a list of the dependecies and loop over this list with lapply. Furthermore, the version number for the packages 'network3D' and 'png' seem to be out-of-date. Could you not leave out the version numbers from the install script? The 'p_load' function of the 'pacman' package updates automatically. `################################################################################

Define list of package names and required versions.

################################################################################ deppkgs = as.list(c(phyloseq = "1.16.0", biomformat = "1.0.0", shiny = "0.13.2", shinythemes = "1.0.1", ggplot2 = "2.1.0", data.table = "1.9.6", networkD3 = "0.2.10", genefilter = "1.54.0", grid = "3.3.0", gridExtra = "2.2.1", markdown = "0.7.7", rmarkdown = "0.9.6", png = "0.1.7", RColorBrewer = "1.1.2", scales = "0.4.0"))

Loop on package check, install, update\

lapply(deppkgs, pacman::p_load) `

MLABuky commented 6 years ago

I am also having this problem. Was manually installing missing packages until I got to "genefilter" which says is not available for R 3.4.3. Also getting the biocLite error.

install.packages("shiny") Installing package into ‘C:/Users/adhorr0/Documents/R/win-library/3.4’ (as ‘lib’ is unspecified) trying URL 'https://cran.cnr.berkeley.edu/bin/windows/contrib/3.4/shiny_1.0.5.zip' Content type 'application/zip' length 2834819 bytes (2.7 MB) downloaded 2.7 MB

package ‘shiny’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\adhorr0\AppData\Local\Temp\RtmpeQaeyJ\downloaded_packages

shiny::runGitHub("shiny-phyloseq","joey711") Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz Loading required package: shiny Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help The following package is missing. genefilter Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

ADGM commented 5 years ago

I am having this problem also. When I try to install the packages manually I run into a dead-end when I try to install "genefilter" and get this error message:

The following package is missing. genefilter Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

I hope I can be helped with this. Thank you!

ADGM commented 5 years ago

The problem persists in the github install because it still runs the original install.R script without the bugfix. I was able to work around this purgatorial issue by doing the manual install for dependencies then trying the auto-install instructions again.

I am having this problem also. When I try to install the packages manually I run into a dead-end when I try to install "genefilter" and get this error message:

The following package is missing. genefilter Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

I hope I can be helped with this. Thank you!

spholmes commented 5 years ago

Did you try

biocLite(genefilter, suppressUpdates = TRUE)

On Tue, Jan 22, 2019 at 8:30 AM ADGM notifications@github.com wrote:

The problem persists in the github install because it still runs the original install.R script without the bugfix. I was able to work around this purgatorial issue by doing the manual install for dependencies then trying the auto-install instructions again.

I am having this problem also. When I try to install the packages manually I run into a dead-end when I try to install "genefilter" and get this error message:

The following package is missing. genefilter Installation will be attempted... Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found

I hope I can be helped with this. Thank you!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/74#issuecomment-456465783, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvUItMhyXLmiswoXmS6krL8bx8FRIks5vFzy9gaJpZM4Og8VG .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

joey711 / shiny-phyloseq

Problem installing #74

version provided and package not missing, so compare.

version = deppkgs,

Define list of package names and required versions.

Loop on package check, install, update\