Failure to update BiocGenerics in Ubuntu 17.10 from 0.22.1 to 0.23 and higher
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rea ▴ 10
@rea-11244
Last seen 4.7 years ago

Dear All,

I am unable to update package BiocGenerics which is required to install BSgenome.

I tried:

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

and got the following error message:

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘BiocGenerics’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocGenerics_0.24.0.tar.gz'
Content type 'application/x-gzip' length 43393 bytes (42 KB)
==================================================
downloaded 42 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 in apply_hotfix73465(getGeneric("cbind")) :
  hotfix failed for generic function cbind()
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’
* removing ‘/home/multiscale/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’

The downloaded source packages are in
    ‘/tmp/Rtmp88aPPs/downloaded_packages’
installation path not writeable, unable to update packages: BiocGenerics, MASS,
  Matrix, mgcv, rpart
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BiocGenerics’ had non-zero exit status

My session information follow:

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=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocGenerics_0.22.1  BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] httr_1.3.1      compiler_3.4.2  R6_2.2.2        tools_3.4.2     withr_2.1.1    
 [6] curl_3.1        memoise_1.1.0   git2r_0.21.0    digest_0.6.15   devtools_1.13.4

My previous attempts, which all failed, include alos:

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

biocLite("BiocUpgrade") 

 

What attempt could you kindly suggest?

Thank you in advance

 

 

BiocGenerics • 1.1k views
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0
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What is the output of

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

 

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Here's the output 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 in apply_hotfix73465(getGeneric("cbind")) : hotfix failed for generic function cbind() Error : unable to load R code in package ‘BiocGenerics’ ERROR: lazy loading failed for package ‘BiocGenerics’ * removing ‘/home/multiscale/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’ The downloaded source packages are in ‘/tmp/Rtmp88aPPs/downloaded_packages’ installation path not writeable, unable to update packages: BiocGenerics, MASS, Matrix, mgcv, rpart Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘BiocGenerics’ had non-zero exit status
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Be sure to update packages in a 'vanilla' R session with no additional packages attached, e.g., from the comman line

R --vanilla -e 'BiocInstaller::biocLite("BiocGenerics")'

If that fails the next level of solution is to update R to the current version, R-3.4.3; the 'hotfix' referenced in the error message is an attempt to work around a bug in R-3.4.2.

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rea ▴ 10
@rea-11244
Last seen 4.7 years ago

I couldn't understand the first proposal of solution.

I solved the problem by updating R to the latest version by following the instructions at https://cran.r-project.org/bin/linux/ubuntu and by installing the Bioconductor package.

 

 

 

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rea ▴ 10
@rea-11244
Last seen 4.7 years ago

What is the effect of

R --vanilla -e "BiocInstaller::biocLite("BiocGenerics")

It does not seem to open an R session. What should I type in?

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

 

or

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

biocLite("BiocUpgrade") 

 

Thanks

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Use the 'comment' button instead of 'answer'.

I messed up my quotations in the original comment, and have fixed them -- R --vanilla -e '<foo>' starts R without loading .Rprofile / .Renvir / .RData files and then executes the R command <foo>. Glad that you arrived at solution anyway.

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