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Question: problem in loading Deseq2
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gravatar for roghaiyeh.safari
11 days ago by
roghaiyeh.safari0 wrote:

I was working with Deseq2 for months and suddenly I had an error loading that. I tried to fix it but I think I made staff more complecated.  Could anybody give me some advice? I even tried to unstall and reinstall R and Rstudio. But problem still there. 

#> library(DESeq2)
#there is an error i can not load deseq2
#Le chargement a nécessité le package : GenomicRanges
#Error: package ‘S4Vectors’ 0.18.3 is loaded, but >= 0.19.11 is required by ‘GenomicRanges’

# I found this in google """Make sure you do not have any R sessions running.

Start R from the command line, using R --vanilla

Run BiocInstaller::biocValid() and follow directions to update / downgrade individual packages.

Use BiocInstaller:biocLite("S4Vectors") to re-install S4Vectors.

Use library(DESeq2) (no library path) to load DESeq2.

If for some reason you want to install and use packages from a particular library location, do so consistently and in a way that avoids duplicate package installations across active library paths. For instance, set .libPaths() to contain a 'session-specific' library path (e.g., Bioc version 3.4 packages) and a 'system' library path (base and recommended packages only)"""

#I tried to do as it says


BiocInstaller::biocValid()

BiocInstaller:biocLite("S4Vectors")
library(DESeq2)

 

#i had an error Error: object 'BiocInstaller' not found

#then I decided to remove S4Vectores and install again

remove.packages('S4Vectors')

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("S4Vectors", version = "3.8")

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'S4Vectors'
Warning: package ‘S4Vectors’ is in use and will not be installed
Update old packages: 'BiocGenerics', 'GenomeInfoDb', 'IRanges', 'processx', 'units'
Update all/some/none? [a/s/n]:

a

 

also installing the dependency ‘S4Vectors’

 

 

  There are binary versions available but the source versions are later:

         binary source needs_compilation

processx  3.2.0  3.2.1              TRUE

units     0.6-1  0.6-2              TRUE

 

  Binaries will be installed

Warning: packages ‘S4Vectors’, ‘BiocGenerics’, ‘GenomeInfoDb’, ‘IRanges’ are in use and will not be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/processx_3.2.0.zip'

Content type 'application/zip' length 300367 bytes (293 KB)

downloaded 293 KB

 

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/units_0.6-1.zip'

Content type 'application/zip' length 1704363 bytes (1.6 MB)

downloaded 1.6 MB

 

package ‘processx’ successfully unpacked and MD5 sums checked

package ‘units’ successfully unpacked and MD5 sums checked

 

The downloaded binary packages are in

C:\Users\Administrateur\AppData\Local\Temp\Rtmps76hIZ\downloaded_packages

library(DESeq2)# again I had an error
Error: le package ‘S4Vectors’ nécessaire pour ‘DESeq2’, mais est introuvable
#In addition: Warning message:
  #"In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
  #cannot open compressed file 'C:/Program Files/R/R-3.5.1/library/S4Vectors/DESCRIPTION', probable reason 'No such file or directory'

remove.packages('DESeq2') # i tried to remove deseq2 and install it again
#Removing package from ‘C:/Program Files/R/R-3.5.1/library’
#(as ‘lib’ is unspecified)

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("DESeq2", version = "3.8")

 

 

library(DESeq2)# again I have an error

Error: le package ‘S4Vectors’ nécessaire pour ‘DESeq2’, mais est introuvable

In addition: Warning message:

In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :

  cannot open compressed file 'C:/Program Files/R/R-3.5.1/library/S4Vectors/DESCRIPTION', probable reason 'No such file or directory'

> remove.packages('DESeq2')

Removing package from ‘C:/Program Files/R/R-3.5.1/library’

(as ‘lib’ is unspecified)

> if (!requireNamespace("BiocManager", quietly = TRUE))

+ install.packages("BiocManager")

> BiocManager::install("DESeq2", version = "3.8")

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)

Installing package(s) 'DESeq2'

also installing the dependency ‘S4Vectors’

 

Warning: package ‘S4Vectors’ is in use and will not be installed

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/DESeq2_1.22.1.zip'

Content type 'application/zip' length 2552570 bytes (2.4 MB)

downloaded 2.4 MB

 

package ‘DESeq2’ successfully unpacked and MD5 sums checked

 

The downloaded binary packages are in

C:\Users\Administrateur\AppData\Local\Temp\Rtmps76hIZ\downloaded_packages

Update old packages: 'BiocGenerics', 'GenomeInfoDb', 'IRanges', 'processx', 'units'

Update all/some/none? [a/s/n]: 

a

also installing the dependency ‘S4Vectors’

 

 

  There are binary versions available but the source versions are later:

         binary source needs_compilation

processx  3.2.0  3.2.1              TRUE

units     0.6-1  0.6-2              TRUE

 

  Binaries will be installed

Warning: packages ‘S4Vectors’, ‘BiocGenerics’, ‘GenomeInfoDb’, ‘IRanges’ are in use and will not be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/processx_3.2.0.zip'

Content type 'application/zip' length 300367 bytes (293 KB)

downloaded 293 KB

 

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/units_0.6-1.zip'

Content type 'application/zip' length 1704363 bytes (1.6 MB)

downloaded 1.6 MB

 

package ‘processx’ successfully unpacked and MD5 sums checked

package ‘units’ successfully unpacked and MD5 sums checked

 

The downloaded binary packages are in

C:\Users\Administrateur\AppData\Local\Temp\Rtmps76hIZ\downloaded_packages

> library(DESeq2)

Error: le package ‘S4Vectors’ nécessaire pour ‘DESeq2’, mais est introuvable

In addition: Warning message:

In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :

  cannot open compressed file 'C:/Program Files/R/R-3.5.1/library/S4Vectors/DESCRIPTION', probable reason 'No such file or directory'

 

 

 

ADD COMMENTlink modified 11 days ago by Martin Morgan ♦♦ 22k • written 11 days ago by roghaiyeh.safari0
0
gravatar for Martin Morgan
11 days ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

I would guess that your your S4Vectors library is partly removed, probably because an update was attempted when another session was using it. Make sure you have no R sessions running. Use the system file manager to manually remove the S4Vectors directory at C:/Program Files/R/R-3.5.1/library/S4Vectors. Start R and install S4Vectors and then DESeq2

BiocManager::install("S4Vectors")
BiocManager::install("DESeq2")

(Usually it is not necessary to install dependencies separately, but since you are having problems it seems better to walk than to run).

It is not necessary, and strongly discouraged, to run R as administrator; the only scenario would be install a system-wide R as administrator, and then install all other packages as a user. The other packages would be installed in a directory in the user's home, rather than in a system-wide location.

ADD COMMENTlink written 11 days ago by Martin Morgan ♦♦ 22k
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