phenoDisco : estep function not found (mclust)

JustynaZitek commented 3 years ago

Hi, sorry for bothering you but I have a problem with phenoDisco, namely that the estep function was not found even though the mclust package is active. How I can solve this issue? Thanks in advance, Justyna

msnset <- phenoDisco(combined, fcol = "markers", times = 100, GS = 10) Iteration 1 Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6, ... first error: could not find function "estep" In addition: There were 11 warnings (use warnings() to see them) sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
system code page: 1250

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

other attached packages: [1] mclust_5.4.7 pRolocGUI_2.0.0 pRolocdata_1.28.0 pRoloc_1.30.0 BiocParallel_1.24.1 [6] MLInterfaces_1.70.0 cluster_2.1.0 annotate_1.68.0 XML_3.99-0.6 AnnotationDbi_1.52.0 [11] IRanges_2.24.1 MSnbase_2.15.7 ProtGenerics_1.22.0 S4Vectors_0.28.1 mzR_2.24.1
[16] Rcpp_1.0.6 Biobase_2.50.0 BiocGenerics_0.36.0

loaded via [1] snow_0.4-3 [5] splines_4.0.4 [9] htmltools_0.5.1.1 [13] memoise_2.0.0 [17] recipes_0.1.15 [21] prettyunits_1.1.1 [25] xfun_0.22 [29] hexbin_1.28.2 [33] glue_1.4.2 [37] kernlab_0.9-29 [41] DBI_1.1.1 [45] progress_1.2.2 [49] lava_1.6.9 [53] sampling_2.9 [57] ellipsis_0.3.1 [61] nnet_7.3-15 [65] tidyselect_1.1.0 [69] later_1.1.0.1 [73] cachem_1.0.4 [77] fastmap_1.1.0 [81] bit64_4.0.5 [85] ncdf4_1.17 [89] biomaRt_2.46.3 [93] affyio_1.60.0 [97] lattice_0.20-41 [101] pillar_1.5.1 [105] MALDIquant_1.19.3 [109] pcaMethods_1.82.0 [113] codetools_0.2-18 [117] assertthat_0.2.1 [121] hms_1.0.0 [125] coda_0.19-4 [129] shiny_1.6.0 a namespace (and not attached): BiocFileCache_1.14.0 plyr_1.8.6 shinydashboard_0.7.1
ggplot2_3.3.3 digest_0.6.27 foreach_1.5.1
viridis_0.5.1 fansi_0.4.2 magrittr_2.0.1
doParallel_1.0.16 mixtools_1.2.0 limma_3.46.0
gower_0.2.2 askpass_1.1 lpSolve_5.6.15
colorspace_2.0-0 blob_1.2.1 rappdirs_0.3.3
dplyr_1.0.5 jsonlite_1.7.2 crayon_1.4.1
impute_1.64.0 survival_3.2-7 iterators_1.0.13
gtable_0.3.0 ipred_0.9-11 zlibbioc_1.36.0
scales_1.1.1 vsn_3.58.0 mvtnorm_1.1-1
miniUI_0.1.1.1 viridisLite_0.3.0 xtable_1.8-4
bit_4.0.4 proxy_0.4-25 preprocessCore_1.52.1
prodlim_2019.11.13 DT_0.17 htmlwidgets_1.5.3
httr_1.4.2 FNN_1.1.3 RColorBrewer_1.1-2
pkgconfig_2.0.3 shinydashboardPlus_2.0.0 sass_0.3.1
dbplyr_2.1.0 utf8_1.2.1 caret_6.0-86
shinyhelper_0.3.2 rlang_0.4.10 reshape2_1.4.4
munsell_0.5.0 tools_4.0.4 LaplacesDemon_16.1.4
generics_0.1.0 RSQLite_2.2.4 stringr_1.4.0
mzID_1.28.0 ModelMetrics_1.2.2.2 knitr_1.31
purrr_0.3.4 randomForest_4.6-14 dendextend_1.14.0
nlme_3.1-152 mime_0.10 xml2_1.3.2
compiler_4.0.4 curl_4.3 e1071_1.7-6
tibble_3.1.0 bslib_0.2.4 stringi_1.5.3
Matrix_1.3-2 shinyjs_2.0.0 vctrs_0.3.6
lifecycle_1.0.0 BiocManager_1.30.10 jquerylib_0.1.3
data.table_1.14.0 httpuv_1.5.5 R6_2.5.0
affy_1.68.0 promises_1.2.0.1 gridExtra_2.3
colourpicker_1.1.0 MASS_7.3-53 gtools_3.8.2
openssl_1.4.3 shinyWidgets_0.6.0 withr_2.4.1
grid_4.0.4 rpart_4.1-15 timeDate_3043.102
class_7.3-18 segmented_1.3-3 pROC_1.17.0.1
lubridate_1.7.10

warnings() Warning messages: 1: In serialize(data, node$con) : 'package:stats' may not be available when loading 2: In serialize(data, node$con) : 'package:stats' may not be available when loading 3: In serialize(data, node$con) : 'package:stats' may not be available when loading 4: In serialize(data, node$con) : 'package:stats' may not be available when loading 5: In serialize(data, node$con) : 'package:stats' may not be available when loading 6: In serialize(data, node$con) : 'package:stats' may not be available when loading 7: In serialize(data, node$con) : 'package:stats' may not be available when loading 8: In serialize(data, node$con) : 'package:stats' may not be available when loading 9: In serialize(data, node$con) : 'package:stats' may not be available when loading 10: In serialize(data, node$con) : 'package:stats' may not be available when loading 11: stop worker failed: attempt to select less than one element in OneIndex

lgatto commented 3 years ago

That's weird indeed. I also have mclust version 5.4.7 and mclust::estep is available.

Could you try to load it with library(mclust) and report any issues, and also check that mclust::estep prints out the body of the function.
If the above are successful, could you re-run phenoDisco() with BPPARAM = BiocParallel::SerialParam().

JustynaZitek commented 3 years ago

Hi Laurent, your suggestion helped, so far it is running , thanks a lot :)

lgatto / pRoloc

phenoDisco : estep function not found (mclust) #140