Entering edit mode
Hi DEP package maintainers,
I am getting an error message when trying to load one of your shiny apps. It looks like the code tries to execute a function from MSnbase that does not exist or is not exported.
> library(DEP)
> run_app("LFQ")
Loading required package: shiny
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'
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] shinydashboard_0.7.2 SummarizedExperiment_1.24.0 Biobase_2.54.0
[4] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[7] S4Vectors_0.32.3 BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[10] matrixStats_0.61.0 tibble_3.1.6 shiny_1.7.1
[13] DEP_1.16.0 gmm_1.6-6 sandwich_3.0-1
[16] dplyr_1.0.8 readr_2.1.2
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 rjson_0.2.21 ellipsis_0.3.2 circlize_0.4.14
[5] XVector_0.34.0 GlobalOptions_0.1.2 clue_0.3-60 rstudioapi_0.13
[9] mzR_2.28.0 affyio_1.64.0 DT_0.21 bit64_4.0.5
[13] fansi_1.0.2 mvtnorm_1.1-3 codetools_0.2-18 ncdf4_1.19
[17] doParallel_1.0.17 impute_1.68.0 knitr_1.37 cluster_2.1.2
[21] vsn_3.62.0 png_0.1-7 BiocManager_1.30.16 compiler_4.1.2
[25] assertthat_0.2.1 Matrix_1.4-0 fastmap_1.1.0 limma_3.50.1
[29] cli_3.2.0 later_1.3.0 htmltools_0.5.2 tools_4.1.2
[33] gtable_0.3.0 glue_1.6.2 GenomeInfoDbData_1.2.7 affy_1.72.0
[37] Rcpp_1.0.8 MALDIquant_1.21 vctrs_0.3.8 preprocessCore_1.56.0
[41] iterators_1.0.14 tmvtnorm_1.4-10 xfun_0.29 mime_0.12
[45] lifecycle_1.0.1 XML_3.99-0.9 rawrr_1.2.0 zlibbioc_1.40.0
[49] MASS_7.3-55 zoo_1.8-9 scales_1.1.1 vroom_1.5.7
[53] MSnbase_2.20.4 pcaMethods_1.86.0 hms_1.1.1 promises_1.2.0.1
[57] ProtGenerics_1.26.0 parallel_4.1.2 protViz_0.7.0 RColorBrewer_1.1-2
[61] ComplexHeatmap_2.10.0 yaml_2.3.5 ggplot2_3.3.5 foreach_1.5.2
[65] BiocParallel_1.28.3 shape_1.4.6 rlang_1.0.1 pkgconfig_2.0.3
[69] bitops_1.0-7 imputeLCMD_2.0 mzID_1.32.0 fontawesome_0.2.2
[73] evaluate_0.15 lattice_0.20-45 purrr_0.3.4 htmlwidgets_1.5.4
[77] bit_4.0.4 tidyselect_1.1.2 norm_1.0-9.5 plyr_1.8.6
[81] magrittr_2.0.2 R6_2.5.1 generics_0.1.2 DelayedArray_0.20.0
[85] DBI_1.1.2 pillar_1.7.0 withr_2.4.3 MsCoreUtils_1.6.2
[89] RCurl_1.98-1.6 crayon_1.5.0 utf8_1.2.2 tzdb_0.2.0
[93] rmarkdown_2.11 GetoptLong_1.0.5 grid_4.1.2 digest_0.6.29
[97] xtable_1.8-4 tidyr_1.2.0 httpuv_1.6.5 munsell_0.5.0
>
A function named imputeMethods() exists in MSCoreUtils
> MsCoreUtils::imputeMethods()
[1] "bpca" "knn" "QRILC" "MLE" "MinDet" "MinProb" "min" "zero" "mixed" "nbavg"
[11] "with" "none"
A code bug?
Best, Tobi
Here is traceback of the error:
Looks like somebody else already reported this error, see Bioc issue, but the DEP package maintainer(s) don't seem to react (>14 days). How is this handled in general?