Invalid row.names length error in error models

[djchin25]

I ran scde about 6 months ago on a small dataset (Fluidigm C1 data) with an older scde version but just installed R-3.3.3 with the latest scde-1.99.2 with the proper flexmix package. Now with a 4810-cell dataset, i'm getting this classification error after a 5-hr run time on a box using 16 of 32-cores (128gb memory).

....snippped.... Classification: weighted 1 Log-likelihood : -12124.1522 2 Log-likelihood : -12011.5585 3 Log-likelihood : -12124.4153 4 Log-likelihood : -12124.4519 5 Log-likelihood : -12124.4040 6 Log-likelihood : -12124.3947 converged ERROR fitting of 10 out of 2778 cells resulted in errors reporting remaining 2768 cells Error in row.names<-.data.frame(*tmp*, value = value) : invalid 'row.names' length Calls: scde.error.models ... rownames<- -> row.names<- -> row.names<-.data.frame

Note: this error was found previously in https://github.com/hms-dbmi/scde/issues/7 but the original poster solved the problem with a fresh R-3.2.1 installation. My sessionInfo is below

R version 3.3.3 (2017-03-06) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final)

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] scde_1.99.1 flexmix_2.3-13 lattice_0.20-35

loaded via a namespace (and not attached): [1] Rcpp_0.12.10 nloptr_1.0.4
[3] RColorBrewer_1.1-2 Lmoments_1.2-3
[5] base64enc_0.1-3 BatchJobs_1.6
[7] iterators_1.0.8 tools_3.3.3
[9] lme4_1.1-13 digest_0.6.12
[11] RSQLite_1.1-2 memoise_1.1.0
[13] checkmate_1.8.2 nlme_3.1-131
[15] mgcv_1.8-17 Matrix_1.2-10
[17] foreach_1.4.3 DBI_0.6-1
[19] parallel_3.3.3 SparseM_1.77
[21] RcppArmadillo_0.7.600.1.0 stringr_1.2.0
[23] extRemes_2.0-8 MatrixModels_0.4-1
[25] stats4_3.3.3 grid_3.3.3
[27] nnet_7.3-12 Biobase_2.26.0
[29] distillery_1.0-2 Rook_1.1-1
[31] fail_1.3 BiocParallel_1.0.3
[33] minqa_1.2.4 limma_3.22.7
[35] car_2.1-4 sendmailR_1.2-1
[37] magrittr_1.5 edgeR_3.8.6
[39] splines_3.3.3 backports_1.0.5
[41] BBmisc_1.11 pcaMethods_1.56.0
[43] codetools_0.2-15 modeltools_0.2-21
[45] BiocGenerics_0.12.1 MASS_7.3-47
[47] pbkrtest_0.4-7 RMTstat_0.3
[49] quantreg_5.33 brew_1.0-6
[51] stringi_1.1.5 rjson_0.2.15
[53] Cairo_1.5-9

[djchin25]

Just noticed that despite downloading and installing 1.99.2, the sessionInfo shows 1.99.1.

[hummuscience]

Getting that same error on scde 1.99.4

R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 17.04

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.7.0 LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] pheatmap_1.0.8 limma_3.34.3
[3] DESeq2_1.18.1 SummarizedExperiment_1.8.0 [5] DelayedArray_0.4.1 matrixStats_0.52.2
[7] Biobase_2.38.0 GenomicRanges_1.30.0
[9] GenomeInfoDb_1.14.0 IRanges_2.12.0
[11] S4Vectors_0.16.0 BiocGenerics_0.24.0
[13] scde_1.99.4 flexmix_2.3-13
[15] lattice_0.20-35

loaded via a namespace (and not attached): [1] nlme_3.1-131 bitops_1.0-6
[3] pbkrtest_0.4-7 bit64_0.9-7
[5] devtools_1.13.4 RColorBrewer_1.1-2
[7] httr_1.3.1 tools_3.4.2
[9] backports_1.1.1 R6_2.2.2
[11] rpart_4.1-11 DBI_0.7
[13] Hmisc_4.0-3 lazyeval_0.2.1
[15] mgcv_1.8-22 colorspace_1.3-2
[17] nnet_7.3-12 withr_2.1.0
[19] gridExtra_2.3 bit_1.1-12
[21] curl_3.0 compiler_3.4.2
[23] git2r_0.19.0 quantreg_5.34
[25] htmlTable_1.11.0 Cairo_1.5-9
[27] SparseM_1.77 scales_0.5.0
[29] checkmate_1.8.5 genefilter_1.60.0
[31] Lmoments_1.2-3 stringr_1.2.0
[33] digest_0.6.12 foreign_0.8-69
[35] minqa_1.2.4 distillery_1.0-4
[37] XVector_0.18.0 base64enc_0.1-3
[39] pkgconfig_2.0.1 htmltools_0.3.6
[41] lme4_1.1-14 extRemes_2.0-8
[43] htmlwidgets_0.9 rlang_0.1.4
[45] RSQLite_2.0 rstudioapi_0.7
[47] BiocInstaller_1.28.0 bindr_0.1
[49] BiocParallel_1.12.0 acepack_1.4.1
[51] dplyr_0.7.4 car_2.1-6
[53] RCurl_1.95-4.8 magrittr_1.5
[55] modeltools_0.2-21 GenomeInfoDbData_0.99.1
[57] Formula_1.2-2 Matrix_1.2-11
[59] Rcpp_0.12.14 munsell_0.4.3
[61] stringi_1.1.6 edgeR_3.20.1
[63] MASS_7.3-47 zlibbioc_1.24.0
[65] plyr_1.8.4 blob_1.1.0
[67] grid_3.4.2 splines_3.4.2
[69] annotate_1.56.1 locfit_1.5-9.1
[71] knitr_1.17 tcltk_3.4.2
[73] rjson_0.2.15 geneplotter_1.56.0
[75] XML_3.98-1.9 glue_1.2.0
[77] RcppArmadillo_0.8.300.1.0 latticeExtra_0.6-28
[79] data.table_1.10.4-3 pcaMethods_1.70.0
[81] nloptr_1.0.4 MatrixModels_0.4-1
[83] purrr_0.2.4 gtable_0.2.0
[85] RMTstat_0.3 tidyr_0.7.2
[87] assertthat_0.2.0 ggplot2_2.2.1
[89] xtable_1.8-2 survival_2.41-3
[91] tibble_1.3.4 AnnotationDbi_1.40.0
[93] memoise_1.1.0 bindrcpp_0.2
[95] cluster_2.0.6 Rook_1.1-1
[97] brew_1.0-6