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Question: Deseq2 no package Matrix found
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gravatar for victoria.carla.moris
7 weeks ago by
victoria.carla.moris0 wrote:

Hi,

I am trying to install the package Deseq2 in Rstudio (on windows 10).

I get an error due to one package which is not found : Matrix

Here is the erro message (sorry it is in French)

>library(DESeq2)
Le chargement a nécessité le package : SummarizedExperiment
Error: package or namespace load failed for ‘SummarizedExperiment’ in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 aucun package nommé ‘Matrix’ n'est trouvé
Error: le package ‘SummarizedExperiment’ ne peut être chargé

I also checked this bioValid and got that one package is out of date.

> biocValid()

* sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=French_Belgium.1252  LC_CTYPE=French_Belgium.1252    LC_MONETARY=French_Belgium.1252 LC_NUMERIC=C                    LC_TIME=French_Belgium.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DelayedArray_0.2.7   matrixStats_0.52.2   Biobase_2.36.2       GenomicRanges_1.28.5 GenomeInfoDb_1.12.2  IRanges_2.10.3       S4Vectors_0.14.4    
[8] BiocGenerics_0.22.0  BiocInstaller_1.26.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6            zlibbioc_1.22.0         XVector_0.16.0          tools_3.4.1             RCurl_1.95-4.8          compiler_3.4.1         
[7] GenomeInfoDbData_0.99.0

* Out-of-date packages
     Package LibPath                                               Installed Built   ReposVer  Repository                            
Rcpp "Rcpp"  "C:/Users/Victoria Moris/Documents/R/win-library/3.4" "0.12.12" "3.4.1" "0.12.13" "https://cran.rstudio.com/src/contrib"

update with biocLite()

Error: 1 package(s) out of date

 

But even after updating I still have the same message.

> biocLite()

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).

Old packages: 'Rcpp'

Update all/some/none? [a/s/n]: 

 

Update all/some/none? [a/s/n]: 

a

 

  There is a binary version available but the source version is later:

      binary  source needs_compilation

Rcpp 0.12.12 0.12.13              TRUE

 

  Binaries will be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/Rcpp_0.12.12.zip'

Content type 'application/zip' length 3319198 bytes (3.2 MB)

downloaded 3.2 MB

 

package ‘Rcpp’ successfully unpacked and MD5 sums checked

 

The downloaded binary packages are in

C:\Users\Victoria Moris\AppData\Local\Temp\Rtmp2HUH0h\downloaded_packages

 

 

 

Let me know how I can solve this problem.

Thank you for your help

ADD COMMENTlink modified 6 weeks ago • written 7 weeks ago by victoria.carla.moris0

Here is what happens when I try to reinstall it:

library(DESeq2)
Le chargement a nécessité le package : SummarizedExperiment
Error: package or namespace load failed for ‘SummarizedExperiment’ in loadNamespace(j <- imp[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 aucun package nommé ‘Matrix’ n'est trouvé
Error: le package ‘SummarizedExperiment’ ne peut être chargé

ADD REPLYlink written 6 weeks ago by victoria.carla.moris0

That’s just trying to load the package. You should try to re-install it with biocLite

ADD REPLYlink written 6 weeks ago by Michael Love14k

It = SummarizedExperiment 

ADD REPLYlink written 6 weeks ago by Michael Love14k
0
gravatar for Michael Love
6 weeks ago by
Michael Love14k
United States
Michael Love14k wrote:

Can you show what happens when you try to reinstall the package that the error message mentions, SummarizedExperiment?

ADD COMMENTlink written 6 weeks ago by Michael Love14k

Ok I try to reinstall everything and now this step works (SummarizedExperiment) as well as "Matrix finally :)!

Then, I tried to install Deseq2. But sill got an error message for "checkmate"

 

library(DESeq2)
Le chargement a nécessité le package : S4Vectors
Le chargement a nécessité le package : stats4
Le chargement a nécessité le package : BiocGenerics
Le chargement a nécessité le package : parallel

Attachement du package : ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min


Attachement du package : ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Le chargement a nécessité le package : IRanges
Le chargement a nécessité le package : GenomicRanges
Le chargement a nécessité le package : GenomeInfoDb
Le chargement a nécessité le package : SummarizedExperiment
Le chargement a nécessité le package : Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Le chargement a nécessité le package : DelayedArray
Le chargement a nécessité le package : matrixStats

Attachement du package : ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


Attachement du package : ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from ‘package:base’:

    apply

Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 aucun package nommé ‘checkmate’ n'est trouvé

 

I tried to install checkmate individually :

> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
> library(checkmate)
Error in library(checkmate) : 
  aucun package nommé ‘checkmate’ n'est trouvé

 

It is not found.

Thank you for your help!

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by victoria.carla.moris0

You should keep trying to install missing packages with biocLite() until there are no more errors. This doesn't usually occur, as all dependencies are installed when you first install, e.g. DESeq2, but it seems like something may have changed on your system, and now those dependencies are missing.

ADD REPLYlink written 6 weeks ago by Michael Love14k

Thank you.

It worked after several tries and errors.

 

ADD REPLYlink written 15 days ago by victoria.carla.moris0
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