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Question: Problem installing BiocGenerics
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gravatar for p.janitza
29 days ago by
p.janitza50
p.janitza50 wrote:

Hello,

when I try to install standrad bioconductor packages with 

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

then I get following error messages: 

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’
* removing ‘/home/philipp/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’
ERROR: dependency ‘BiocGenerics’ is not available for package ‘S4Vectors’
* removing ‘/home/philipp/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
ERROR: dependency ‘BiocGenerics’ is not available for package ‘Biobase’
* removing ‘/home/philipp/R/x86_64-pc-linux-gnu-library/3.4/Biobase’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’ are not available for package ‘IRanges’
* removing ‘/home/philipp/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/philipp/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’

The downloaded source packages are in
	‘/tmp/RtmppId7uG/downloaded_packages’
Warnmeldungen:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BiocGenerics’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘S4Vectors’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘Biobase’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IRanges’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status

I couldn't find a solution during my search through the internet. I'm using freshly installed Ubuntu 17.10 and R 3.4.2 (2017-09-28) -- "Short Summer".

Thanks in advance!

ADD COMMENTlink modified 28 days ago • written 29 days ago by p.janitza50
1

I get the same error messages with $ R --vanilla!

 

R version 3.4.2 (2017-09-28) -- "Short Summer"

Copyright (C) 2017 The R Foundation for Statistical Computing

Platform: x86_64-pc-linux-gnu (64-bit)



>  library("BiocInstaller")

Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help


> biocLite('BiocGenerics')

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.2 (2017-09-28).

Installing package(s) ‘BiocGenerics’

versuche URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/BiocGenerics_0.22.1.tar.gz'

Content type 'application/x-gzip' length 42943 bytes (41 KB)

==================================================

downloaded 41 KB


* installing *source* package ‘BiocGenerics’ ...

** R

** inst

** preparing package for lazy loading

Creating a new generic function for ‘append’ in package ‘BiocGenerics’

Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’

Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’

Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE

Error : unable to load R code in package ‘BiocGenerics’

ERROR: lazy loading failed for package ‘BiocGenerics’

* removing ‘/home/philipp/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’


The downloaded source packages are in

‘/tmp/RtmpsxuCwM/downloaded_packages’

Warnmeldung:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘BiocGenerics’ had non-zero exit status


> sessionInfo()

R version 3.4.2 (2017-09-28)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 17.10


Matrix products: default

BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1

LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1


locale:

 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    

 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   

 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     


other attached packages:

[1] BiocInstaller_1.26.1


loaded via a namespace (and not attached):

[1] compiler_3.4.2 tools_3.4.2   
ADD REPLYlink written 28 days ago by p.janitza50
1

Well, the problematic code is in relation to A: BiocGenerics built with R 3.4.2 changes behaviour , a regression (bug) in the released version of R and an attempt to patch it in BiocGenerics. Something about your particular set-up (not the version of ubuntu) is causing problems. I'm running short of ideas.

It might be helpful to know how you installed R. It could be the locale ('de_DE.UTF-8'), so you could try

$ locale -a  # returns several values, perhaps including en_US.UTF-8 and C
$ LC_ALL=en_US.UTF-8 R --vanilla

where 'en_US.UTF-8' or simply "C" is the English-language or plain C encoding returned by locale -a.

Another option is to install the patched version of R-3-4-2, from source (R-patched) downloaded from https://stat.ethz.ch/R/daily/ following https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Simple-compilation (this may require installation of system libraries; if you installed R using apt-get, satisfy these by installing r-base-dev instead of r-base). 

We will continue to work on this on our end.

ADD REPLYlink written 28 days ago by Martin Morgan ♦♦ 20k

Try the more modest

biocLite("BiocGenerics")

and report the output of that command and the command

sessionInfo()
ADD REPLYlink modified 29 days ago • written 29 days ago by Martin Morgan ♦♦ 20k

Thank you for your answer - here is the output: 

R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


> library("BiocInstaller", lib.loc="~/R/x86_64-pc-linux-gnu-library/3.4")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help

> biocLite("BiocGenerics")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.2 (2017-09-28).
Installing package(s) ‘BiocGenerics’
versuche URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/BiocGenerics_0.22.1.tar.gz'
Content type 'application/x-gzip' length 42943 bytes (41 KB)
==================================================
downloaded 41 KB

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’
* removing ‘/home/philipp/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’

The downloaded source packages are in
	‘/tmp/Rtmpm6wNq2/downloaded_packages’
Warnmeldung:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BiocGenerics’ had non-zero exit status

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.26.1

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2   
 
 

 

ADD REPLYlink written 29 days ago by p.janitza50

I can't reproduce this error. Can you repeat by starting R in the command line and with the '--vanilla' flag?

$ R --vanilla

ADD REPLYlink written 29 days ago by Martin Morgan ♦♦ 20k

Hi,

I can't reproduce this either. Glad that installing R 3.4.2 Patched solved the problem. If you still have your R 3.4.2 installation around, could you start it and show us the output of methods:::.standardGenericDots?

FWIW I just made a small change to the hotfix code to improve the error message in case of failure. With this change the error message will report the name of the generic function for which the hotfix failed. The change is in the devel version of BiocGenerics only (version 0.23.4). The release version (0.22.1) was frozen a few days ago.

H.

ADD REPLYlink modified 28 days ago • written 28 days ago by Hervé Pagès ♦♦ 13k
1
gravatar for p.janitza
28 days ago by
p.janitza50
p.janitza50 wrote:

Using different encoding didn't work for me.
Installing the patch version solved my problem! Now using this version:

R version 3.4.2 Patched (2017-10-12 r73560) -- "Short Summer

thanks for your help!

ADD COMMENTlink modified 28 days ago • written 28 days ago by p.janitza50

Even I was facing the same problem on Ubuntu 17.10.

I installed BiocGenerics using:

$ sudo apt-get install r-bioc-biocgenerics

And biocLite() worked successfully after this.

ADD REPLYlink written 26 days ago by ishanee.india0
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