Error in trying to use Interactive analysis using the DEP Shiny apps (LFQ app)
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0
Entering edit mode
@e6f804c9
Last seen 7 months ago
United Kingdom

Hello there,

I have installed the DEP package and the DEP library and when I try to run the LFQ app I get the following error:

Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'

The MSnbase package is installed.

Is there any possible fix?

Thank you in advance.

In more detail:

```

library("DEP")

Warning message: In fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.8). This might lead to errors when loading mzR. If you encounter such issues, please send a report, including the output of sessionInfo() to the Bioc support forum at https://support.bioconductor.org/. For details see also https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

run_app("LFQ")

Loading required package: shiny

Attaching package: ‘dplyr’

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

filter, lag

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

intersect, setdiff, setequal, union

Loading required package: MatrixGenerics Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

count

Attaching package: ‘MatrixGenerics’

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

colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods,
colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians,
colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates,
colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars,
rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians,
rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates,
rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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

combine, intersect, setdiff, union

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.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

first, rename

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

expand.grid, I, unname

Loading required package: IRanges

Attaching package: ‘IRanges’

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

collapse, desc, slice

Loading required package: GenomeInfoDb 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")'.

Attaching package: ‘Biobase’

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

rowMedians

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

anyMissing, rowMedians

Attaching package: ‘shinydashboard’

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

box

Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'

LFQ • 394 views
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Entering edit mode

Hi Maria,

I think it would be helpful if you would tag your issue with the respective package name, see posting guide and properly embed your code.

Best, Tobi

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Entering edit mode
Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 3 days ago
United States

issue is acknowledged with workaround patch here: https://github.com/arnesmits/DEP/issues/26

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