MLSeq package error

Question

[jonessara770]

Hello,

I would like to use MLSeq package but I am getting this error.

> library(MLSeq)
Error : object ‘bag.default’ is not exported by 'namespace:caret'
Error: package or namespace load failed for ‘MLSeq’

would you please help me to overcome this error?

Thanks

Sara

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.1 (Sierra)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
 [1] edgeR_3.14.0               randomForest_4.6-12        limma_3.28.21              DESeq2_1.12.4              SummarizedExperiment_1.2.3 Biobase_2.32.0             GenomicRanges_1.24.3      
 [8] GenomeInfoDb_1.8.7         IRanges_2.6.1              S4Vectors_0.10.3           BiocGenerics_0.18.0        caret_6.0-72               ggplot2_2.1.0              lattice_0.20-34           

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7          locfit_1.5-9.1       digest_0.6.10        foreach_1.4.3        plyr_1.8.4           chron_2.3-47         acepack_1.4.1        MatrixModels_0.4-1   RSQLite_1.0.0       
[10] zlibbioc_1.18.0      minqa_1.2.4          data.table_1.9.6     annotate_1.50.1      SparseM_1.72         car_2.1-3            nloptr_1.0.4         rpart_4.1-10         Matrix_1.2-7.1      
[19] splines_3.3.1        lme4_1.1-12          BiocParallel_1.6.6   geneplotter_1.50.0   stringr_1.1.0        foreign_0.8-67       RCurl_1.95-4.8       munsell_0.4.3        mgcv_1.8-15         
[28] htmltools_0.3.5      nnet_7.3-12          gridExtra_2.2.1      htmlTable_1.7        Hmisc_4.0-0          codetools_0.2-15     XML_3.98-1.4         MASS_7.3-45          bitops_1.0-6        
[37] ModelMetrics_1.1.0   grid_3.3.1           nlme_3.1-128         xtable_1.8-2         gtable_0.2.0         DBI_0.5-1            magrittr_1.5         scales_0.4.0         stringi_1.1.2       
[46] XVector_0.12.1       reshape2_1.4.2       genefilter_1.54.2    latticeExtra_0.6-28  Formula_1.2-1        RColorBrewer_1.1-2   iterators_1.0.8      tools_3.3.1          pbkrtest_0.4-6      
[55] survival_2.40-1      AnnotationDbi_1.34.4 colorspace_1.2-7     cluster_2.0.5        knitr_1.14           quantreg_5.29

Answer 1

[gokmen.zararsiz]

The error arises from importing "bag.default" function in caret. NAMESPACE is fixed in the development version 1.15.1. You can download the source files from https://github.com/Bioconductor-mirror/MLSeq. With the upcoming version 1.16.0, namespace error will be fixed in the released version.