Error in using interactive analysis using the DEP Shiny apps

[anuragraj]

Hi there,

I am facing an issue when trying to start the interactive session analysis.

library("DEP")

For LFQ analysis

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
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: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'

The DEP library is perfectly loading after installation and MSnbase package is also installed.

The session info for the same:

sessionInfo(package = NULL)
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
[1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8
[4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] shinydashboard_0.7.1 SummarizedExperiment_1.22.0 Biobase_2.52.0
[4] GenomicRanges_1.44.0 GenomeInfoDb_1.28.1 IRanges_2.26.0
[7] S4Vectors_0.30.0 BiocGenerics_0.38.0 MatrixGenerics_1.4.2
[10] matrixStats_0.60.1 tibble_3.1.4 dplyr_1.0.7
[13] shiny_1.6.0 DEP_1.14.0

loaded via a namespace (and not attached):
[1] ProtGenerics_1.24.0 bitops_1.0-7 doParallel_1.0.16 RColorBrewer_1.1-2
[5] MSnbase_2.18.0 tools_4.1.1 DT_0.18 utf8_1.2.2
[9] R6_2.5.1 affyio_1.62.0 tmvtnorm_1.4-10 DBI_1.1.1
[13] colorspace_2.0-2 GetoptLong_1.0.5 withr_2.4.2 tidyselect_1.1.1
[17] compiler_4.1.1 preprocessCore_1.54.0 Cairo_1.5-12.2 DelayedArray_0.18.0
[21] sandwich_3.0-1 scales_1.1.1 mvtnorm_1.1-2 readr_2.0.1
[25] affy_1.70.0 digest_0.6.27 XVector_0.32.0 pkgconfig_2.0.3
[29] htmltools_0.5.2 fastmap_1.1.0 limma_3.48.3 htmlwidgets_1.5.3
[33] rlang_0.4.11 GlobalOptions_0.1.2 impute_1.66.0 shape_1.4.6
[37] generics_0.1.0 zoo_1.8-9 mzID_1.30.0 BiocParallel_1.26.2
[41] RCurl_1.98-1.4 magrittr_2.0.1 GenomeInfoDbData_1.2.6 MALDIquant_1.20
[45] Matrix_1.3-4 Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
[49] MsCoreUtils_1.4.0 imputeLCMD_2.0 lifecycle_1.0.0 vsn_3.60.0
[53] MASS_7.3-54 zlibbioc_1.38.0 plyr_1.8.6 grid_4.1.1
[57] promises_1.2.0.1 crayon_1.4.1 lattice_0.20-44 hms_1.1.0
[61] circlize_0.4.13 mzR_2.26.1 ComplexHeatmap_2.8.0 pillar_1.6.2
[65] rjson_0.2.20 codetools_0.2-18 XML_3.99-0.7 glue_1.4.2
[69] pcaMethods_1.84.0 BiocManager_1.30.16 httpuv_1.6.2 tzdb_0.1.2
[73] png_0.1-7 vctrs_0.3.8 foreach_1.5.1 tidyr_1.1.3
[77] gtable_0.3.0 purrr_0.3.4 clue_0.3-59 norm_1.0-9.5
[81] assertthat_0.2.1 ggplot2_3.3.5 mime_0.11 xtable_1.8-4
[85] later_1.3.0 ncdf4_1.17 iterators_1.0.13 gmm_1.6-6
[89] cluster_2.1.2 ellipsis_0.3.2

[luizalmeida93]

I've got the same issue.

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

Any news on a possible fix?

[mariakokolaki]

I am facing the same problem on macOS Catalina 10.15.7.

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

Any news?

[anuragraj]

I have found a solution to the issue. There was an issue of missing imputeMethod() in MSnbase, but no such method is available in the package.
This method is available in the MsCoreUtils package.
So, you can go to the R DEP installed directory and find "app.R" which may be available at path "~/R/x86_64-pc-linux-gnu-library/4.1/DEP/shiny_apps/LFQ".

Edit the app.R file on line no 34 from
choices = c("man", MSnbase::imputeMethods())[1:9],
to this line
choices = c("man", MsCoreUtils::imputeMethods())[1:9],

This will allow the shiny app to run.
Hope this will help.

[kamilanykiel]

Have the same problem. Thanks @anuragraj for the fix, but editing a code installation is not a viable fix. Was this added to the package source code? If not, this issue should be reopened.