Remote access installation issues - 'non-zero exist'

[Peter Mcerlean]

Hi RnBeads Team,

I've been trying to install Rnbeads onto my PC at work via remote access (via MAC).

I've had various issues with dependencies not installing and have tried various ways to solve it; reinstall, run as administrator, install missing packages individually (e.g. Tibble) and the suggestion posted here:  https://bioinformatics.stackexchange.com/questions/3143/installing-rnbeads-via-bioconductor-onload-failed-in-loadnamespace-call-n 

However, I'm stalled again on some of the dependencies being 'not available (for R version 3.6.3)'.

I tried installing an older R version but then other dependancies now don't work (e.g. ggplot2 written in R3.6.3).

Is there a work around for this or should I contact the author of the missing packages to update them accordingly?

Kind regards,

Peter

Example output:

Old packages: 'class', 'foreign', 'lattice', 'nlme', 'nnet', 'survival'

Update all/some/none? [a/s/n]: n

Error: package or namespace load failed for 'ggplot2' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called 'tibble'

Error: package 'ggplot2' could not be loaded

In addition: Warning messages:

1: In install.packages(...) :

  installation of package 'TxDb.Hsapiens.UCSC.hg19.knownGene' had non-zero exit status

2: In install.packages(...) :

  installation of package 'tibble' had non-zero exit status

3: In install.packages(...) :

  installation of package 'IlluminaHumanMethylationEPICmanifest' had non-zero exit status

4: In install.packages(...) :

  installation of package 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19' had non-zero exit status

5: In install.packages(...) :

  installation of package 'IlluminaHumanMethylation450kmanifest' had non-zero exit status

6: In install.packages(...) :

  installation of package 'IlluminaHumanMethylation450kanno.ilmn12.hg19' had non-zero exit status

7: In install.packages(...) :

  installation of package 'FDb.InfiniumMethylation.hg19' had non-zero exit status

> library(RnBeads)

Loading required package: ggplot2

Error: package or namespace load failed for 'ggplot2' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called 'tibble'

Error: package 'ggplot2' could not be loaded

> install.packages('tibble')

Installing package into 'C:/Program Files/R/Library'

(as 'lib' is unspecified)

--- Please select a CRAN mirror for use in this session ---

  There is a binary version available but the source version is later:

       binary source needs_compilation

tibble  2.1.3  3.0.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) n

trying URL 'https://cran.ma.imperial.ac.uk/bin/windows/contrib/3.6/tibble_2.1.3.zip'

Content type 'application/zip' length 337382 bytes (329 KB)

downloaded 329 KB

package 'tibble' successfully unpacked and MD5 sums checked

The downloaded binary packages are in

        C:\Users\pmcerlea\AppData\Local\Temp\Rtmp0M70K8\downloaded_packages

> library(RnBeads)

Loading required package: ggplot2

Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: gridExtra

Attaching package: 'gridExtra'

The following object is masked from 'package:BiocGenerics':

    combine

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: matrixStats

Loading required package: illuminaio

Loading required package: methylumi

Loading required package: Biobase

Welcome to Bioconductor

    Vignettes contain introductory material; view with

    'browseVignettes()'. To cite Bioconductor, see

    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: scales

Loading required package: reshape2

Error: package 'FDb.InfiniumMethylation.hg19' required by 'methylumi' could not be found

[Michael Scherer]

Hi Peter,

Indeed, there are currently some problems with RnBeads dependencies depending on you computational setup. Here are some suggestions on how to solve this issue:

• Install the stringi package from GitHub rather than from CRAN. This solved some issues for me: devtools::install_github("gagolews/stringi")
• Use the RnBeads installation script for a successful installation: source("http://rnbeads.org/data/install.R")
• Alternatively: Use the RnBeads conda container (conda install bioconductor-rnbeads) or the RnBeads Docker image (https://quay.io/repository/biocontainers/bioconductor-rnbeads?tab=tags)

I hope that one of these solutions works for you. Let me know if there is another issue.




Best,




Michael

[Peter Mcerlean]

Dear Michael,

I took the first two suggestions above and everything seems to be working so far!

I think the issue was the Stringi package as I also installed it on my MAC and now the analysis runs more completely (saving a me few more forum posts!).

Of note though for Stingi installation, I used CRAN version for PC and GitHub for MAC.

Kind regards,

Peter