incredible difficulty in installing 'scde' on R3.4.3 and R3.5.1

[tanpuekai]

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:

adjusting
library size based on 2000 entries
cell : calculating cell-cell similarities ... done
fitting cell models:
cell.1 : IS0802-100
Error in new("FLXMRglmCf", FLXMRglmC(..., family = family), mu = mu) :
could not find function "new"
cell.2 : IS0802-102
Error in new("FLXMRglmCf", FLXMRglmC(..., family = family), mu = mu) :
could not find function "new"
cell.3 : IS0802-103

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:

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /software/R/3.4.3/lib64/R/lib/libRblas.so
LAPACK: /software/R/3.4.3/lib64/R/lib/libRlapack.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] stats graphics grDevices utils datasets base

other attached packages:
[1] scde_2.6.0 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

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:

install.packages(c("Cairo","Rcpp","Rook","rjson","RColorBrewer","RMTstat","extRemes","quantreg"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("RcppArmadillo","edgeR","pcaMethods","BiocParallel"))
install.packages("modeltools")
install.packages("devtools")
require(devtools)
devtools::install_version('flexmix', '2.3-13')
biocLite("scde")

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:

adjusting library size based on 2000 entries
cell : calculating cell-cell similarities ... done
fitting cell models:
cell.1 : IS0802-42
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE
cell.2 : IS0802-43
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “expression” is not valid for slot ‘defineComponent’ in an object of class “FLXMRglmC”; is(value, "expressionOrfunction") is not TRUE
cell.3 : IS0802-45

My windows PC has these sessionInfo:

R version 3.5.1 (2018-07-02)
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 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] scde_2.8.0 Cairo_1.5-9 usethis_1.4.0 devtools_2.0.0 flexmix_2.3-13 lattice_0.20-35 BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.19 locfit_1.5-9.1 prettyunits_1.0.2 ps_1.2.0 assertthat_0.2.0 rprojroot_1.3-2
[7] digest_0.6.18 R6_2.3.0 cellranger_1.1.0 backports_1.1.2 MatrixModels_0.4-1 stats4_3.5.1
[13] pillar_1.3.0 rlang_0.3.0.1 curl_3.2 readxl_1.1.0 data.table_1.11.8 SparseM_1.77
[19] car_3.0-2 callr_3.0.0 Matrix_1.2-14 desc_1.2.0 BiocParallel_1.14.2 foreign_0.8-70
[25] RMTstat_0.3 distillery_1.0-4 compiler_3.5.1 pkgconfig_2.0.2 extRemes_2.0-9 BiocGenerics_0.26.0
[31] base64enc_0.1-3 pkgbuild_1.0.2 mgcv_1.8-24 pcaMethods_1.72.0 nnet_7.3-12 tibble_1.4.2
[37] edgeR_3.22.5 Lmoments_1.2-3 rio_0.5.10 crayon_1.3.4 withr_2.1.2 MASS_7.3-50
[43] grid_3.5.1 nlme_3.1-137 magrittr_1.5 zip_1.0.0 cli_1.0.1 carData_3.0-2
[49] RcppArmadillo_0.9.100.5.0 fs_1.2.6 remotes_2.0.1 limma_3.36.5 brew_1.0-6 openxlsx_4.1.0
[55] rjson_0.2.20 RColorBrewer_1.1-2 tools_3.5.1 forcats_0.3.0 Biobase_2.40.0 glue_1.3.0
[61] Rook_1.1-1 hms_0.4.2 abind_1.4-5 processx_3.2.0 pkgload_1.0.1 parallel_3.5.1
[67] sessioninfo_1.1.0 memoise_1.1.0 haven_1.1.2 quantreg_5.36 modeltools_0.2-22

can you pls see how to address these?

[tanpuekai]

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!

[SystemsBiologist]

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