shiny-phyloseq issues

[jaycodyk]

Hello, I have been able to use phyloseq-shiny with no issues until today. Earlier I tried to launch the package and got a message indicating that I needed to update R to the latest version. I updated to R version 3.3.0 and tried to launch shiny-phyloseq: shiny::runGitHub("shiny-phyloseq","joey711") And got the following: Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz Bioconductor version 3.3 (BiocInstaller 1.22.1), ?biocLite for help Bioconductor version 3.3 (BiocInstaller 1.22.1), ?biocLite for help Bioconductor version 3.3 (BiocInstaller 1.22.1), ?biocLite for help Bioconductor version 3.3 (BiocInstaller 1.22.1), ?biocLite for help Error in message("The following package is missing.\n", missingPackages, : object 'missingPackages' not found

I tried to reinstall all required packages but I still get the message. Any help is much appreciated. Thanks

[dejmail]

I also have this problem, and can confirm that having the packages installed seems to make no difference. Running Bioconductor version 3.3 (BiocInstaller 1.22.2) on Linux.

From the code, shouldn't missingPackages be missingPackage ? This doesn't fix all the the error but at least goes onto the next one, which from the traceback is

Error in match(x, table, nomatch = 0L) : object 'i' not found 
5 match(x, table, nomatch = 0L) 
4 "BiocUpgrade" %in% pkgs 
3 biocLite(i, suppressUpdates = TRUE) 
2 (function (pkg, version = NULL, verbose = TRUE) 
{
    availpacks = .packages(all.available = TRUE)
    source("http://bioconductor.org/biocLite.R") ... 
1 mapply(names(deppkgs), FUN = install_missing_packages, version = deppkgs, 
    USE.NAMES = TRUE) 

I've tried to determine where in the function it is having trouble, but I'm not managing. I'm still not very knowledgeable with R.

[joey711]

I'll push a fix...

[joey711]

This should be fixed now. Please post if not and I'll re-open this issue.

[dejmail]

Thanks for the bugfix. I still can't run the program though. It seems no matter if _shiny_ has just been installed using the command from the website

install.packages("shiny") shiny::runGitHub("shiny-phyloseq","joey711")

I still get immediately after that

Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz
Loading required package: shiny
Bioconductor version 3.3 (BiocInstaller 1.22.2), ?biocLite for help
The following package is missing.
phyloseq
Installation will be attempted...

and error with the following stacktrace. I don't know if this is the same thing that the first poster is experiencing.

 Error in match(x, table, nomatch = 0L) : object 'i' not found 
17 match(x, table, nomatch = 0L) 
16 "BiocUpgrade" %in% pkgs 
15 biocLite(i, suppressUpdates = TRUE) at install.R#42
14 (function (pkg, version = NULL, verbose = TRUE) 
{
    availpacks = .packages(all.available = TRUE)
    source("http://bioconductor.org/biocLite.R") ... 
13 mapply(install_missing_packages, pkg = names(deppkgs), version = deppkgs, 
    MoreArgs = list(verbose = TRUE), SIMPLIFY = FALSE, USE.NAMES = TRUE) at install.R#64
12 eval(expr, envir, enclos) 
11 eval(ei, envir) 
10 withVisible(eval(ei, envir)) 
9 source("install.R", local = TRUE) 
8 ..stacktraceon..({
    source("install.R", local = TRUE)
    source("core/default-parameters.R", local = TRUE)
    simpletime = function() { ... 
7 eval(expr, envir, enclos) 
6 eval(exprs, envir) 
5 sourceUTF8(file.path.ci(appDir, "global.R")) 
4 appParts$onStart() 
3 runApp(appdir, ...) 
2 runUrl(url, subdir = subdir, destdir = destdir, ...) 
1 shiny::runGitHub("shiny-phyloseq", "joey711") 

I've tried running the command with debug, but haven't quite got it to work.

[jaycodyk]

@dejmail I am not sure how to fix the issue that you are having now. The fix from @joey711 solved the issue for me. There was several packages I installed, including reinstalling:

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

Now shiny-phyloseq launches without issues.

[dejmail]

Hi. Yes, sorry I was being silly. Once I installed libcurl4-openssl-dev and libxml2-dev, I installed "phyloseq" and its dependency packages and shiny-phyloseq works now.

[joey711]

Glad to hear it!

I imagined it had something to do with the latest versions of phyloseq, biomformat, and related BioC packages that just got released in the last few weeks, including the latest version of R.

[HSapers]

Hi, I'm rather new to using R, I had used shiny without issues, upon updating to the new version of R I seem to be having the same problem with being unable to install phyloseq. Any help would be appreciated - thanks!

> devtools::source_url("https://raw.githubusercontent.com/joey711/shiny-phyloseq/master/install.R")
SHA-1 hash of file is 5299b7e2db2851420210b5b1baf58a6ef8525e48
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
The following package is missing.
phyloseq
Installation will be attempted...
Error in match(x, table, nomatch = 0L) : object 'i' not found
> 

[jaycodyk]

Did you try to reinstall the packages required by phyloseq? I went back to http://joey711.github.io/shiny-phyloseq/Install.html and did a complete reinstall of Shiny. You have to make sure you overwrite the old packages. That fixed the issue for me.

[HSapers]

Thank you

I tried

install.packages("shiny")
shiny::runGitHub("shiny-phyloseq","joey711")

with the output:

Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz
Loading required package: shiny
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Current version of package
phyloseq    1.14.0
is less than required.
                Update will be attempted.
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘biomformat’
Warning: package ‘biomformat’ is not available (for R version 3.3.1)
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
The following package is missing.
biomformat
Installation will be attempted...
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘biomformat’
Warning: package ‘biomformat’ is not available (for R version 3.3.1)
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Current version of package
ggplot2 2.0.0
is less than required.
                Update will be attempted.
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘biomformat’
Warning: package ‘biomformat’ is not available (for R version 3.3.1)
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Current version of package
genefilter  1.52.1
is less than required.
                Update will be attempted.
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘biomformat’
Warning: package ‘biomformat’ is not available (for R version 3.3.1)
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Current version of package
rmarkdown   0.9.5
is less than required.
                Update will be attempted.
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘biomformat’
Warning: package ‘biomformat’ is not available (for R version 3.3.1)
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning: BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
Current version of package
scales  0.3.0
is less than required.
                Update will be attempted.
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘biomformat’
Warning: package ‘biomformat’ is not available (for R version 3.3.1)
phyloseq package version:
1.14.0
Error in library(i, character.only = TRUE) : 
  there is no package called ‘biomformat’

The updates do not seem to be overwriting outdated packages. Is there a way to make sure this happens, or should I manually go and delete old versions?

thanks Haley

[jaycodyk]

What happens if you type: install.packages("biomformat")

[HSapers]

> install.packages("biomformat")
Installing package into ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘biomformat’ is not available (for R version 3.3.1)

[spholmes]

It's a BioC package so needs to be installed via BioClite

On Wed, Jul 20, 2016 at 11:00 AM, HSapers notifications@github.com wrote:

install.packages("biomformat") Installing package into ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘biomformat’ is not available (for R version 3.3.1)

— 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/66#issuecomment-234029949, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvVmITcMgwqoDkY04dmWZRUjNzSQPks5qXmIwgaJpZM4Ice5n .

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/

[jaycodyk]

@spholmes Does that mean the following has to be installed first?

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

I am running R version 3.3.0. Are you sure the update to 3.3.1 does not have anything to do with it?

[HSapers]

every time I give it a try, there seems to be another 'missing' package:

> library("BiocInstaller", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("biomformat")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘biomformat’
also installing the dependencies ‘zlibbioc’, ‘plyr’, ‘rhdf5’

this seemed to work so tired

> install.packages("shiny")
> shiny::runGitHub("shiny-phyloseq","joey711")

with this result:

Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz
Loading required package: shiny
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
The following package is missing.
phyloseq
Installation will be attempted...

 Error in match(x, table, nomatch = 0L) : object 'i' not found 

so I tired to manually install phyloseq:

> biocLite("phyloseq")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘phyloseq’
also installing the dependencies ‘pkgmaker’, ‘registry’, ‘rngtools’, ‘gridBase’, ‘colorspace’, ‘doParallel’, ‘stringi’, ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘chron’, ‘iterators’, ‘gtable’, ‘magrittr’, ‘NMF’, ‘irlba’, ‘stringr’, ‘RColorBrewer’, ‘dichromat’, ‘munsell’, ‘labeling’, ‘permute’, ‘BiocGenerics’, ‘ade4’, ‘ape’, ‘Biostrings’, ‘data.table’, ‘foreach’, ‘ggplot2’, ‘igraph’, ‘multtest’, ‘reshape2’, ‘scales’, ‘vegan’, ‘Biobase’

and then again

> install.packages("shiny")
> shiny::runGitHub("shiny-phyloseq","joey711")

and now

The following package is missing.
shinythemes
Installation will be attempted...
 Error in match(x, table, nomatch = 0L) : object 'i' not found