Question

problem with DESeq2

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melikabakharzi • 0

@melikabakharzi-23244

Last seen 5.6 years ago

Hi, I use this code for install Biocmanager and then DESeq2 packages and I got these errors. what is the problem?

install.packages("BiocManager") Installing package into ‘C:/Users/melika/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/BiocManager_1.30.10.zip' Content type 'application/zip' length 99006 bytes (96 KB) downloaded 96 KB

package ‘BiocManager’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\melika\AppData\Local\Temp\RtmpgVb1KM\downloaded_packages

BiocManager::install("DESeq2") Bioconductor version 3.7 (BiocManager 1.30.10), R 3.5.2 (2018-12-20) Installing package(s) 'DESeq2' trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/DESeq2_1.20.0.zip' Content type 'application/zip' length 2524898 bytes (2.4 MB) downloaded 2.4 MB

package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\melika\AppData\Local\Temp\RtmpgVb1KM\downloaded_packages Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, survival Old packages: 'quantreg' Update all/some/none? [a/s/n]: n

library("DESeq2") Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘scales’

What is the problem? BioManager or DESeq2? What can I do to fix it?

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252
[3] LCMONETARY=EnglishUnited States.1252 LCNUMERIC=C
[5] LCTIME=English_United States.1252

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

other attached packages: [1] SummarizedExperiment1.10.1 DelayedArray0.6.6
[3] BiocParallel1.14.2 matrixStats0.56.0
[5] Biobase2.40.0 GenomicRanges1.32.7
[7] GenomeInfoDb1.16.0 IRanges2.14.12
[9] S4Vectors0.18.3 BiocGenerics0.26.0

loaded via a namespace (and not attached): [1] Rcpp1.0.4 Formula1.2-3 XVector0.20.0
[4] splines3.5.2 zlibbioc1.26.0 lattice0.20-38
[7] rlang0.4.5 tools3.5.2 grid3.5.2
[10] gtable0.3.0 survival2.43-3 Matrix1.2-15
[13] GenomeInfoDbData1.1.0 BiocManager1.30.10 bitops1.0-6
[16] RCurl1.98-1.1 compiler_3.5.2

deseq2 • 1.9k views

ADD COMMENT • link updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by melikabakharzi • 0

score 0 · Answer 1 · 2020-04-02

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Michael Love 43k

@mikelove

Last seen 2 days ago

United States

You'll need to first debug installation of scales. Once you can do library(scales) then re-attempt DESeq2 installation.

ADD COMMENT • link 5.6 years ago Michael Love 43k

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Hi Michael, Thank you for your advice. I installed "scales" package and library that, but I get warnings. and DESeq2 package installation also faced with a problem. Here are my codes:

install.packages("scales") Installing package into ‘C:/Users/melika/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/scales_1.1.0.zip' Content type 'application/zip' length 549827 bytes (536 KB) downloaded 536 KB

package ‘scales’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\melika\AppData\Local\Temp\RtmpK85LK5\downloaded_packages

library("scales") Warning message: package ‘scales’ was built under R version 3.5.3 BiocManager::install("DESeq2") Bioconductor version 3.7 (BiocManager 1.30.10), R 3.5.2 (2018-12-20) Installing package(s) 'DESeq2' trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/DESeq2_1.20.0.zip' Content type 'application/zip' length 2524898 bytes (2.4 MB) downloaded 2.4 MB

package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\melika\AppData\Local\Temp\RtmpK85LK5\downloaded_packages Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, survival Old packages: 'backports', 'classInt', 'lme4', 'quantreg', 'sf', 'spData' Update all/some/none? [a/s/n]: n

ADD REPLY • link 5.6 years ago melikabakharzi • 0

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I don't see a problem here necessarily:

package ‘DESeq2’ successfully unpacked and MD5 sums checked...

Can you try

library(DESeq2)

ADD REPLY • link 5.6 years ago Michael Love 43k

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I tried this I got an error. Is this a problem that R said for example "this" object is masked from "this"?

library("DESeq2") Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel

Attaching 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, basename, cbind, colMeans,
colnames, colSums, dirname, 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

Attaching package: ‘S4Vectors’

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

expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

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

windows

Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor

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

Loading required package: DelayedArray Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

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

colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

aperm, apply

Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘glue’ In addition: Warning message: package ‘matrixStats’ was built under R version 3.5.3

ADD REPLY • link 5.6 years ago melikabakharzi • 0

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So you are back to square one: “glue” is not installed. You can repeat these steps until there are no missing packages.

This is not how installation works when the Bioc instructions are followed 100% of the time so I wonder if you would be better off starting from scratch. But this would involve custom instructions and the simplest thing for you to do at this point with just to be keep installing missing packages.

ADD REPLY • link 5.6 years ago Michael Love 43k