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enriquea / feseR

feseR: Combining feature selection methods for analyzing omics data
https://github.com/enriquea/feseR
GNU General Public License v2.0
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rJava dependency? #4

Closed ravichas closed 5 years ago

ravichas commented 5 years ago

Hello feseR team: Is there a rJava dependency on combineFS call? I am running into rJava installation issues. Thanks Ravi

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_rt.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] doParallel_1.0.14 iterators_1.0.10 foreach_1.4.4 feseR_0.2.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 pillar_1.4.0 compiler_3.5.2 [4] gower_0.2.0 plyr_1.8.4 tools_3.5.2 [7] class_7.3-15 digest_0.6.19 rpart_4.1-15 [10] ipred_0.9-9 lubridate_1.7.4 tibble_2.1.1 [13] nlme_3.1-139 gtable_0.3.0 lattice_0.20-38 [16] pkgconfig_2.0.2 rlang_0.3.4 Matrix_1.2-17 [19] prodlim_2018.04.18 withr_2.1.2 stringr_1.4.0 [22] dplyr_0.8.0.1 globals_0.12.4 generics_0.0.2 [25] recipes_0.1.5 stats4_3.5.2 grid_3.5.2 [28] caret_6.0-84 nnet_7.3-12 tidyselect_0.2.5 [31] data.table_1.12.2 glue_1.3.1 listenv_0.7.0 [34] R6_2.4.0 survival_2.44-1.1 lava_1.6.5 [37] reshape2_1.4.3 ggplot2_3.1.1 purrr_0.3.2 [40] magrittr_1.5 ModelMetrics_1.2.2 scales_1.0.0 [43] codetools_0.2-16 MASS_7.3-51.4 splines_3.5.2 [46] randomForest_4.6-14 assertthat_0.2.1 future_1.13.0 [49] timeDate_3043.102 colorspace_1.4-1 stringi_1.4.3 [52] lazyeval_0.2.2 munsell_0.5.0 crayon_1.3.4

enriquea commented 5 years ago

Hi @ravichas ,

Some of the imported packages require rJava...Below how looks a typical R session after running a combineFS example without any issue.

> sessionInfo()

R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                  LC_TIME=de_DE.UTF-8           LC_COLLATE=en_US.UTF-8        LC_MONETARY=de_DE.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=de_DE.UTF-8          LC_NAME=de_DE.UTF-8           LC_ADDRESS=de_DE.UTF-8        LC_TELEPHONE=de_DE.UTF-8      LC_MEASUREMENT=de_DE.UTF-8    LC_IDENTIFICATION=de_DE.UTF-8

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

other attached packages:
 [1] doParallel_1.0.14 iterators_1.0.10  foreach_1.4.4     ROCR_1.0-7        gplots_3.0.1.1    caret_6.0-84      ggplot2_3.1.1     lattice_0.20-38   feseR_0.2.0       rJava_0.9-11

Best,

E.

ravichas commented 5 years ago

Thanks. I managed to install rJava and I am fine.