No dunkley2006params, no makeGoSet

[blue-moon22]

Things highlighted in bold may be relevant to the problem

library("MSnbase") 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, xtabs

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

anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unlist, unsplit

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")'.

Loading required package: mzR Loading required package: Rcpp Loading required package: BiocParallel Loading required package: ProtGenerics

This is MSnbase version 1.18.1 Read '?MSnbase' and references therein for information about the package and how to get started.

Attaching package: ‘MSnbase’

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

smooth

library("pRoloc") Loading required package: MLInterfaces Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Loading required package: XML Loading required package: cluster Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘genefilter’ Error: package ‘MLInterfaces’ could not be loaded library("pRolocdata")

This is pRolocdata version 1.8.0. Use 'pRolocdata()' to list available data sets.

data(dunkley2006params) Warning message: In data(dunkley2006params) : data set ‘dunkley2006params’ not found ?makeGoSet No documentation for ‘makeGoSet’ in specified packages and libraries: you could try ‘??makeGoSet’ sessionInfo() R version 3.2.4 (2016-03-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages: [1] pRolocdata_1.8.0 cluster_2.0.3 annotate_1.48.0 XML_3.98-1.4
[5] AnnotationDbi_1.32.3 IRanges_2.4.8 S4Vectors_0.8.11 MSnbase_1.18.1
[9] ProtGenerics_1.2.1 BiocParallel_1.4.3 mzR_2.4.1 Rcpp_0.12.3
[13] Biobase_2.30.0 BiocGenerics_0.16.1 BiocInstaller_1.20.1

loaded via a namespace (and not attached): [1] vsn_3.38.0 splines_3.2.4 sfsmisc_1.1-0 foreach_1.4.3
[5] threejs_0.2.1 shiny_0.13.1 assertthat_0.1 affy_1.48.0
[9] robustbase_0.92-5 impute_1.44.0 RSQLite_1.0.0 lattice_0.20-33
[13] limma_3.26.8 digest_0.6.9 gbm_2.1.1 colorspace_1.2-6
[17] htmltools_0.3 httpuv_1.3.3 preprocessCore_1.32.0 rda_1.0.2-2
[21] plyr_1.8.3 mlbench_2.1-1 MALDIquant_1.14 zlibbioc_1.16.0
[25] xtable_1.8-2 mvtnorm_1.0-5 scales_0.4.0 affyio_1.40.0
[29] ggplot2_2.1.0 ggvis_0.4.2 nnet_7.3-12 survival_2.38-3
[33] magrittr_1.5 mime_0.4 mclust_5.1 doParallel_1.0.10
[37] MASS_7.3-45 class_7.3-14 tools_3.2.4 trimcluster_0.1-2
[41] stringr_1.0.0 kernlab_0.9-23 munsell_0.4.3 fpc_2.1-10
[45] lambda.r_1.1.7 pls_2.5-0 pcaMethods_1.60.0 mzID_1.8.0
[49] futile.logger_1.4.1 grid_3.2.4 iterators_1.0.8 htmlwidgets_0.6
[53] base64enc_0.1-3 gtable_0.2.0 codetools_0.2-14 flexmix_2.3-13
[57] DBI_0.3.1 reshape2_1.4.1 R6_2.1.2 prabclus_2.2-6
[61] dplyr_0.4.3 futile.options_1.0.0 modeltools_0.2-21 stringi_1.0-1
[65] rpart_4.1-10 DEoptimR_1.0-4 diptest_0.75-7

[blue-moon22]

Fixed! it's in pRolocGUI

[lgatto]

The dunkley2006params data and makeGoSet function are in pRoloc, not the GUI.

[blue-moon22]

yes of course, apologies