Question

DESeq2 - cannot find function?

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lindsay • 0

@lindsay-23095

Last seen 5.6 years ago

Hello all:

I am trying to use DESeq2 in R. I try to install the library through bioconductor, but then receive the following errors:

Loading required package: GenomeInfoDb Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’ Error: package ‘GenomeInfoDb’ could not be loaded

and

dds <- DESeqDataSetFromTximport(txi, met, ~condition) Error in DESeqDataSetFromTximport(txi, met, ~condition) : could not find function "DESeqDataSetFromTximport" test = DESeq(dds) Error in DESeq(dds) : could not find function "DESeq" res = results(test) Error in results(test) : could not find function "results"

Within the DESeq package.

To solve the error I have uninstalled and tried install.packages(DESeq2), and BiocManager::install(DESeq2) and am still not able to download the package fully and execute my command. Is this a permissions issue, or an issue with the package or my path/data?

deseq2 r software error • 2.1k views

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

score 0 · Answer 1 · 2020-03-12

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Michael Love 43k

@mikelove

Last seen 4 days ago

United States

The first error is the one to focus on.

Try installing the missing package manually (only install Bioc packages with BiocManager by the way).

ADD COMMENT • link 5.6 years ago Michael Love 43k

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Thank you for your reply! I tried installing "GenomeInfoDb" manually through "packages" and used the zip files, however I am receiving another error message:

library(GenomicRanges) 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, colnames, dirname, do.call, duplicated, eval,
evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

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

Error: package ‘GenomeInfoDb’ required by ‘GenomicRanges’ could not be found

install.packages("C:/Users/Lindsay's PC/Downloads/GenomeInfoDbData1.2.2.tar.gz", repos = NULL, type = "source") Installing package into ‘C:/Users/Lindsay's PC/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) * installing *source* package 'GenomeInfoDbData' ... ** using staged installation ** data ** inst ** help * installing help indices converting help for package 'GenomeInfoDbData' finding HTML links ... done GenomeInfoDbData-package html
** building package indices ** testing if installed package can be loaded from temporary location * arch - i386 Error: unexpected symbol in "tools:::.testloadpackage('GenomeInfoDbData', 'C:/Users/Lindsay's" Execution halted *** arch - x64 Error: unexpected symbol in "tools:::.testloadpackage('GenomeInfoDbData', 'C:/Users/Lindsay's" Execution halted ERROR: loading failed for 'i386', 'x64' * removing 'C:/Users/Lindsay's PC/Documents/R/win-library/3.6/GenomeInfoDbData' Warning in install.packages : installation of package ‘C:/Users/LINDSA~1/DOWNLO~1/GenomeInfoDbData1.2.2.tar.gz’ had non-zero exit status install.packages("C:/Users/Lindsay's PC/Downloads/GenomeInfoDb1.22.0.tar.gz", repos = NULL, type = "source") Installing package into ‘C:/Users/Lindsay's PC/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) ERROR: dependency 'GenomeInfoDbData' is not available for package 'GenomeInfoDb' * removing 'C:/Users/Lindsay's PC/Documents/R/win-library/3.6/GenomeInfoDb' Warning in install.packages : installation of package ‘C:/Users/LINDSA~1/DOWNLO~1/GenomeInfoDb1.22.0.tar.gz’ had non-zero exit status

ADD REPLY • link 5.6 years ago lindsay • 0

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I tried installing "GenomeInfoDb" manually through "packages" and used the zip files...

Do not do this! You will create errors that we cannot help you with. Again, only use BiocManager for Bioconductor.

ADD REPLY • link 5.6 years ago Michael Love 43k