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’:
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’:
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’:
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’:
The following objects are masked from ‘package:base’:
Loading required package: IRanges
Attaching package: ‘IRanges’
The following objects are masked from ‘package:dplyr’:
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’:
The following objects are masked from ‘package:matrixStats’:
Attaching package: ‘shinydashboard’
The following object is masked from ‘package:graphics’:
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