Error package or namespace load failed for MAIT
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Entering edit mode
thomas • 0
@thomas-13864
Last seen 4.1 years ago

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        

MAIT agricolae • 632 views
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Entering edit mode
shepherl 2.8k
@lshep
Last seen 1 day ago
United States

Unfortunately the MAIT package is marked for deprecation and will no longer be supported by Bioconductor.  The package maintainers have been unresponsive and their package has been broken in both current release and devel versions of Bioconductor for quite some time.  You may reach out to the maintainers directly if you feel so inclined. 

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