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Question: Biocgenerics updating problem on ubuntu 17.10
0
gravatar for siinemselvi
19 days ago by
siinemselvi0 wrote:

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

ADD COMMENTlink modified 19 days ago • written 19 days ago by siinemselvi0

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 REPLYlink written 19 days ago by shepherl ♦♦ 510
> 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 REPLYlink written 19 days ago by siinemselvi0
0
gravatar for siinemselvi
19 days ago by
siinemselvi0 wrote:
 

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

 

 

ADD COMMENTlink written 19 days ago by siinemselvi0

Based on this message

```

installation path not writeable, unable to update packages: Rcpp, BiocGenerics

```

I would guess that there might be some permissions issues on the directories you are trying to write.  Please check the results of  `.libPaths()`  and check where `BiocGenerics` is installed (`ls -l` on the results of .libPaths()).  There may be more than one directory, and the directory where it is installed might not be writable (perhaps only accessible via root?) 

You could also try removing the package until it says no more installs and reinstall: 

```

remove.packages("BiocGenerics")

biocLite("BiocGenerics")

```

 

 

 

ADD REPLYlink written 16 days ago by shepherl ♦♦ 510
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