Question

Biocgenerics updating problem on ubuntu 17.10

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siinemselvi • 0

@siinemselvi-14461

Last seen 7.0 years ago

Hi,
In R to use other packages Biocgenerics should be updated from 0.22 to 0.23.3. But in ubuntu the last version of r-bioc-biocgenerics is 0.22. I couldnt uptade from ubuntu and R. please can you help me

bioconductor biocgenerics ubuntu package updates r update • 2.4k views

ADD COMMENT • link 7.0 years ago siinemselvi • 0

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Could you please provide more information? Include the commands you tried to use to update BiocGenerics with the output they produce as well as the results of sessionInfo()

ADD REPLY • link 7.0 years ago shepherl 4.1k

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> 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=tr_TR.UTF-8       LC_NUMERIC=C               LC_TIME=tr_TR.UTF-8       
 [4] LC_COLLATE=tr_TR.UTF-8     LC_MONETARY=tr_TR.UTF-8    LC_MESSAGES=tr_TR.UTF-8   
 [7] LC_PAPER=tr_TR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=tr_TR.UTF-8 LC_IDENTIFICATION=C       

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

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

on ubuntu;

~$ sudo apt-get install r-bioc-biocgenerics
[sudo] password for sinem: 
Paket listeleri okunuyor... Bitti(Done)
Bağımlılık ağacı oluşturuluyor       
Durum bilgisi okunuyor... Bitti(Done)      
r-bioc-biocgenerics zaten en yeni sürümde(the lastversion) (0.22.1-1ubuntu1).
Aşağıdaki paketler otomatik olarak kurulmuş ve artık bu paketlere gerek duyulmuyor(packages are no need anymore):
  r-cran-codetools r-cran-lattice r-cran-spatial
Bu paketleri kaldırmak için 'sudo apt autoremove' komutunu kullanın.
0 paket yükseltilecek, 0 yeni paket kurulacak, 0 paket kaldırılacak ve 2 paket yükseltilmeyecek.

ADD REPLY • link 7.0 years ago siinemselvi • 0

score 0 · Answer 1 · 2017-11-24

As an example when I try to install AnnatotionDbi;

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("AnnotationDbi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘AnnotationDbi’
also installing the dependencies ‘BiocGenerics’, ‘IRanges’, ‘S4Vectors’
.
.
.
.

installing to /home/sinem/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘BiocGenerics’ 0.22.1 was found, but >= 0.23.3 is required by ‘S4Vectors’
ERROR: lazy loading failed for package ‘S4Vectors’
* removing ‘/home/sinem/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/sinem/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/sinem/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’

The downloaded source packages are in
‘/tmp/RtmpqetLrx/downloaded_packages’
installation path not writeable, unable to update packages: Rcpp, BiocGenerics
Warning messages:
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 ‘IRanges’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status

 When İ try to update on R

> update.packages(BiocGenerics)
Error in update.packages(BiocGenerics) : 
  'BiocGenerics' couldnt found
> update.packages(biocLite())
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’

.
.
.

installing to /home/sinem/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘BiocGenerics’ 0.22.1 was found, but >= 0.23.3 is required by ‘S4Vectors’
ERROR: lazy loading failed for package ‘S4Vectors’
* removing ‘/home/sinem/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/home/sinem/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/sinem/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’

The downloaded source packages are in
	‘/tmp/RtmpqetLrx/downloaded_packages’
installation path not writeable, unable to update packages: Rcpp, BiocGenerics
Warning messages:
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 ‘IRanges’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
> update.packages(biocVersion())
Error in list.files(lib) : hatalı 'path' argümanı
> update.packages(biocUpdatePackages())
Error in unique(c(pkgs, deps)) : varsayılanı olmayan "pkgs" argümanı yok