Closed Ivy-ops closed 3 years ago
Hi @Ivy-ops ,
Just to clarify my understanding here: you are running that exact chunk of code on both your local machine and a cluster, and it failed only on the cluster?
Can you try adding inits
(see documentation) to your input?
Hi @bryandmartin ,
Thanks for the feedback.
Yes, you are correct. I installed corncob on cluster and local computer. Error shows on cluster, while running on local computer have no error.
May I please know how to set inits? I see in tutorial.
Optional initializations for model fit using formula and phi.formula as rows of a matrix.
It is embarrassed that I still do not know how to set inits.
Thanks!!
Closing this in response to your email.
For posterioty, it was a package install issue. The solution was to manually install “trust” and “optimr”.
Hi developer,
I encounter below error in applying package on cluster. May I have your help? Thanks! However, I have no problem in running this on my local computer.
My system info:
Matrix products: default BLAS: /usr/lib64/libblas.so.3.4.2 LAPACK: /usr/lib64/liblapack.so.3.4.2
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 methods base
other attached packages: [1] phyloseq_1.34.0 corncob_0.2.0
loaded via a namespace (and not attached): [1] Rcpp_1.0.6 ape_5.5 lattice_0.20-44
[4] prettyunits_1.1.1 Biostrings_2.58.0 assertthat_0.2.1
[7] foreach_1.5.1 utf8_1.2.1 slam_0.1-48
[10] R6_2.5.0 plyr_1.8.6 stats4_4.0.3
[13] ggplot2_3.3.3 pillar_1.6.1 zlibbioc_1.36.0
[16] rlang_0.4.11 progress_1.2.2 rstudioapi_0.13
[19] data.table_1.14.0 vegan_2.5-7 S4Vectors_0.28.1
[22] Matrix_1.3-3 detectseparation_0.2 splines_4.0.3
[25] stringr_1.4.0 igraph_1.2.6 munsell_0.5.0
[28] ROI_1.0-0 numDeriv_2016.8-1.1 compiler_4.0.3
[31] pkgconfig_2.0.3 BiocGenerics_0.36.1 multtest_2.46.0
[34] mgcv_1.8-36 biomformat_1.18.0 tidyselect_1.1.1
[37] tibble_3.1.2 IRanges_2.24.1 codetools_0.2-18
[40] fansi_0.5.0 permute_0.9-5 crayon_1.4.1
[43] dplyr_1.0.6 MASS_7.3-54 rhdf5filters_1.2.1
[46] grid_4.0.3 registry_0.5-1 nlme_3.1-152
[49] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.0
[52] DBI_1.1.1 magrittr_2.0.1 scales_1.1.1
[55] stringi_1.6.2 XVector_0.30.0 reshape2_1.4.4
[58] ellipsis_0.3.2 generics_0.1.0 vctrs_0.3.8
[61] lpSolveAPI_5.5.2.0-17.7 ROI.plugin.lpsolve_1.0-0 Rhdf5lib_1.12.1
[64] iterators_1.0.13 tools_4.0.3 ade4_1.7-16
[67] Biobase_2.50.0 glue_1.4.2 purrr_0.3.4
[70] hms_1.1.0 parallel_4.0.3 survival_3.2-11
[73] colorspace_2.0-1 rhdf5_2.34.0 cluster_2.1.2