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")'.
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)
Things highlighted in bold may be relevant to the problem
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
The following objects are masked from ‘package:stats’:
The following objects are masked from ‘package:base’:
Loading required package: Biobase Welcome to Bioconductor
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’:
This is pRolocdata version 1.8.0. Use 'pRolocdata()' to list available data sets.
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