Trying to use the 'MAIT' package from Bioconductor.
It was OK last week but since, I have troubles with the "agricolae" package ...
This is how to install MAIT:
>source("https://bioconductor.org/biocLite.R")
>biocLite("MAIT")
>library(MAIT)
But then I have this error message:
Loading required package: CAMERA
Loading required package: Biobase
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, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, 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, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: xcms
Loading required package: BiocParallel
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: ProtGenerics
This is MSnbase version 2.2.0
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
The following object is masked from ‘package:base’:
trimws
This is xcms version 1.52.0
Attaching package: ‘xcms’
The following object is masked from ‘package:stats’:
sigma
Loading required package: pls
Attaching package: ‘pls’
The following object is masked from ‘package:stats’:
loadings
Error: package or namespace load failed for ‘MAIT’:
object ‘order.group’ is not exported by 'namespace:agricolae'
In addition: Warning message:
In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.10)
than is installed on your system (0.12.12). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
I understood I had to update the package "agricolae", which I did but same issue, same error ...
A bit annoying as this is something that worked before - and apparently without the agricolae thing.
Thanks for your answers
SessionInfo():
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] pls_2.6-0 CAMERA_1.32.0 xcms_1.52.0 MSnbase_2.2.0 ProtGenerics_1.8.0
[6] mzR_2.10.0 Rcpp_0.12.12 BiocParallel_1.10.1 Biobase_2.36.2 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] nlme_3.1-131 bitops_1.0-6 pbkrtest_0.4-7 plsgenomics_1.5 gmodels_2.16.2
[6] doParallel_1.0.10 RColorBrewer_1.1-2 tools_3.4.1 backports_1.1.0 affyio_1.46.0
[11] AlgDesign_1.1-7.3 rpart_4.1-11 KernSmooth_2.23-15 mgcv_1.8-19 Hmisc_4.0-3
[16] lazyeval_0.2.0 colorspace_1.3-2 nnet_7.3-12 sp_1.2-5 gridExtra_2.2.1
[21] klaR_0.6-12 compiler_3.4.1 MassSpecWavelet_1.42.0 preprocessCore_1.38.1 quantreg_5.33
[26] graph_1.54.0 htmlTable_1.9 expm_0.999-2 SparseM_1.77 caTools_1.17.1
[31] scales_0.5.0 checkmate_1.8.3 affy_1.54.0 RBGL_1.52.0 stringr_1.2.0
[36] digest_0.6.12 minqa_1.2.4 foreign_0.8-69 RhpcBLASctl_0.15-148 base64enc_0.1-3
[41] pkgconfig_2.0.1 htmltools_0.3.6 lme4_1.1-13 limma_3.32.5 maps_3.2.0
[46] htmlwidgets_0.9 rlang_0.1.2 impute_1.50.1 BiocInstaller_1.26.1 combinat_0.0-8
[51] mzID_1.14.0 gtools_3.5.0 spdep_0.6-15 acepack_1.4.1 ModelMetrics_1.1.0
[56] car_2.1-5 magrittr_1.5 Formula_1.2-2 dotCall64_0.9-04 MALDIquant_1.16.4
[61] Matrix_1.2-11 munsell_0.4.3 S4Vectors_0.14.4 vsn_3.44.0 stringi_1.1.5
[66] MASS_7.3-47 zlibbioc_1.22.0 gplots_3.0.1 plyr_1.8.4 grid_3.4.1
[71] gdata_2.18.0 deldir_0.1-14 lattice_0.20-35 splines_3.4.1 multtest_2.32.0
[76] knitr_1.17 igraph_1.1.2 boot_1.3-20 reshape2_1.4.2 codetools_0.2-15
[81] stats4_3.4.1 LearnBayes_2.15 XML_3.98-1.9 latticeExtra_0.6-28 agricolae_1.2-7
[86] pcaMethods_1.68.0 data.table_1.10.4 nloptr_1.0.4 spam_2.1-1 foreach_1.4.3
[91] MatrixModels_0.4-1 gtable_0.2.0 RANN_2.5.1 ggplot2_2.2.1 e1071_1.6-8
[96] coda_0.19-1 class_7.3-14 survival_2.41-3 tibble_1.3.4 iterators_1.0.8
[101] IRanges_2.10.3 fields_9.0 cluster_2.0.6 caret_6.0-76
