Open tanpuekai opened 5 years ago
Is there a workflow that guarantees success of installation and running, for R3.4.3?
I installed (successfully) the developer's version (1.99.4) of scde, and still encountered the same errors in the running:
attached base packages: [1] stats graphics grDevices utils datasets base
other attached packages: [1] scde_1.99.4 flexmix_2.3-13 lattice_0.20-35 devtools_1.13.5
loaded via a namespace (and not attached): [1] modeltools_0.2-22 locfit_1.5-9.1 [3] Rook_1.1-1 haven_1.1.2 [5] carData_3.0-2 stats4_3.4.3 [7] mgcv_1.8-24 rlang_0.3.0.1 [9] pillar_1.3.0 foreign_0.8-70 [11] withr_2.1.2 BiocParallel_1.12.0 [13] BiocGenerics_0.24.0 RColorBrewer_1.1-2 [15] readxl_1.1.0 MatrixModels_0.4-1 [17] extRemes_2.0-9 pcaMethods_1.70.0 [19] cellranger_1.1.0 zip_1.0.0 [21] memoise_1.1.0 RcppArmadillo_0.9.100.5.0 [23] Biobase_2.38.0 rio_0.5.10 [25] forcats_0.3.0 SparseM_1.77 [27] Cairo_1.5-9 quantreg_5.36 [29] parallel_3.4.3 curl_3.2 [31] RMTstat_0.3 methods_3.4.3 [33] Rcpp_0.12.19 edgeR_3.20.9 [35] limma_3.34.9 abind_1.4-5 [37] brew_1.0-6 rjson_0.2.20 [39] hms_0.4.2 digest_0.6.15 [41] openxlsx_4.1.0 distillery_1.0-4 [43] grid_3.4.3 Lmoments_1.2-3 [45] tools_3.4.3 magrittr_1.5 [47] tibble_1.4.2 crayon_1.3.4 [49] car_3.0-2 pkgconfig_2.0.2 [51] MASS_7.3-50 Matrix_1.2-14 [53] data.table_1.11.8 nnet_7.3-12 [55] nlme_3.1-137 compiler_3.4.3 adjusting library size based on 2000 entries cell : calculating cell-cell similarities ... done fitting cell models: cell.1 : IS0802-42 Error in new("FLXMRglmCf", FLXMRglmC(..., family = family), mu = mu) : could not find function "new" cell.2 : IS0802-43 Error in new("FLXMRglmCf", FLXMRglmC(..., family = family), mu = mu) : could not find function "new" cell.3 : IS0802-45 Error in new("FLXMRglmCf", FLXMRglmC(..., family = family), mu = mu) : could not find function "new"
### Thanks a lot!
Hi Tanpuekai, Did you manage to solve the problem? I am facing the same problem but so far I could not solve it in R 3.5.1
Looking forward to hearing from you Best
Hi,
I have previously installed and successfully run your 'scde' package (after many difficulties also, and i couldn't remember how it ended up being successful finally, other than that i also downgrade the 'flexmix' package to 2.3-13 version).
However, our server (Linux based) recently went through some upgrade, and they are now providing R3.4.3 and R3.5.1, instead of the old 3.2.5 that i worked on. I have successfully installed 'scde' package on our server's new R3.4.3 under my own folder (non-admin); and i am still struggling to install 'scde' for its new R3.5.1 on our server as of now. Unfortunately, even for the R3.4.3 that has now a 'scde' installed, as i re-ran my old codes of PAGODA, it reported a lot of errors:
I am aware that these are much the same to some of other issues brought up by other people, but my 'flexmix' has been particularly downgraded to your issue #40 , but never succeed. These are the sessionInf() on our server:
To see if I can install your package from a completely clean R, I downloaded a latest R3.5.1 to my own windows PC, completely clean, and carried out these installation processes:
It did succeed in installing the packages. And i again re-ran my old PAGODA codes on this R3.5.1 on my windows PC, but again it reported these errors:
My windows PC has these sessionInfo:
can you pls see how to address these?