Question

Deseq2 no package Matrix found

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Entering edit mode

victoria.carla.moris • 0

@victoriacarlamoris-14070

Last seen 7.1 years ago

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I also checked this bioValid and got that one package is out of date.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* Out-of-date packages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Error: 1 package(s) out of date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]:

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

deseq2 bioconductor matrix • 2.5k views

ADD COMMENT • link 7.1 years ago victoria.carla.moris • 0

0

Entering edit mode

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 REPLY • link 7.1 years ago victoria.carla.moris • 0

0

Entering edit mode

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

ADD REPLY • link 7.1 years ago Michael Love 42k

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It = SummarizedExperiment

ADD REPLY • link 7.1 years ago Michael Love 42k

score 0 · Answer 1 · 2017-10-01

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Entering edit mode

Michael Love 42k

@mikelove

Last seen 9 hours ago

United States

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

ADD COMMENT • link 7.1 years ago Michael Love 42k

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Entering edit mode

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 REPLY • link 7.1 years ago victoria.carla.moris • 0

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Entering edit mode

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 REPLY • link 7.1 years ago Michael Love 42k

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Entering edit mode

Thank you.

It worked after several tries and errors.

ADD REPLY • link 7.0 years ago victoria.carla.moris • 0