Errors with mclust // collect plot function about cola HOT 7 CLOSED

Can you send me the object rl? It might be the issue related to other packages such as ComplexHeatmap.

Also can you provide your sessionInfo()?

from cola.

Here is the rl object
rl_object.zip

sessionInfo:

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252

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

other attached packages:
[1] genefilter_1.76.0 markdown_1.1 knitr_1.37 cola_2.0.0
[5] viridis_0.6.2 viridisLite_0.4.0 ggrepel_0.9.1 factoextra_1.0.7
[9] ComplexHeatmap_2.10.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[13] purrr_0.3.4 readr_2.0.2 tidyr_1.1.4 tibble_3.1.5
[17] ggplot2_3.3.5 tidyverse_1.3.1

loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.4.1 circlize_0.4.13 repr_1.1.4
[5] splines_4.1.1 GenomeInfoDb_1.30.0 digest_0.6.28 foreach_1.5.1
[9] htmltools_0.5.2 magick_2.7.3 fansi_0.5.0 magrittr_2.0.1
[13] memoise_2.0.0 cluster_2.1.2 doParallel_1.0.16 tzdb_0.2.0
[17] Biostrings_2.62.0 annotate_1.72.0 modelr_0.1.8 matrixStats_0.61.0
[21] colorspace_2.0-2 skimr_2.1.3 blob_1.2.2 rvest_1.0.2
[25] haven_2.4.3 xfun_0.27 crayon_1.4.2 RCurl_1.98-1.5
[29] microbenchmark_1.4.9 jsonlite_1.7.2 impute_1.68.0 brew_1.0-6
[33] survival_3.2-11 iterators_1.0.13 glue_1.4.2 polyclip_1.10-0
[37] gtable_0.3.0 zlibbioc_1.40.0 XVector_0.34.0 GetoptLong_1.0.5
[41] kernlab_0.9-29 shape_1.4.6 prabclus_2.3-2 BiocGenerics_0.40.0
[45] DEoptimR_1.0-10 scales_1.1.1 DBI_1.1.1 Rcpp_1.0.7
[49] xtable_1.8-4 clue_0.3-60 bit_4.0.4 mclust_5.4.9
[53] stats4_4.1.1 httr_1.4.2 RColorBrewer_1.1-2 fpc_2.2-9
[57] modeltools_0.2-23 ellipsis_0.3.2 pkgconfig_2.0.3 XML_3.99-0.8
[61] flexmix_2.3-17 nnet_7.3-16 dbplyr_2.1.1 utf8_1.2.2
[65] tidyselect_1.1.1 rlang_0.4.12 AnnotationDbi_1.56.2 munsell_0.5.0
[69] cellranger_1.1.0 tools_4.1.1 cachem_1.0.6 cli_3.1.0
[73] generics_0.1.1 RSQLite_2.2.8 broom_0.7.11 evaluate_0.14
[77] fastmap_1.1.0 yaml_2.2.1 bit64_4.0.5 fs_1.5.0
[81] robustbase_0.93-9 KEGGREST_1.34.0 slam_0.1-50 xml2_1.3.2
[85] compiler_4.1.1 rstudioapi_0.13 png_0.1-7 reprex_2.0.1
[89] stringi_1.7.5 highr_0.9 lattice_0.20-44 Matrix_1.3-4
[93] vctrs_0.3.8 pillar_1.6.5 lifecycle_1.0.1 BiocManager_1.30.16
[97] eulerr_6.1.1 GlobalOptions_0.1.2 bitops_1.0-7 irlba_2.3.3
[101] R6_2.5.1 gridExtra_2.3 IRanges_2.28.0 diceR_1.1.0
[105] codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1 rjson_0.2.20
[109] withr_2.4.3 S4Vectors_0.32.0 GenomeInfoDbData_1.2.7 diptest_0.76-0
[113] parallel_4.1.1 hms_1.1.1 class_7.3-19 rmarkdown_2.11
[117] skmeans_0.2-14 Biobase_2.54.0 lubridate_1.8.0 base64enc_0.1-3

from cola.

I suggest you to update ComplexHeatmap to the newest version from GitHub. The error message implies it might be a inconsistency to the older version of ComplexHeatmap.

Also please update cola from GitHub. I found a small bug and just fixed it.

I ran cola_report() on your object rl and everything was running smoothly.

from cola.

Thank you for you answer.

I just updated both cola and ComplexHeatmap package but nothing has changed. I also tried to run it in an environment with only these two packages loaded (see the corresponding session info at the end).

The cola_report() function runs (it generates the report), but without any of the graphs produced by the collect plot function.

When running alone the collect_plot function:

> collect_plots(rl, k = 2, fun = consensus_heatmap, cores = 1)
Erreur dans { : task 1 failed - "objet 'fun_name' introuvable"

If the collect plots function works for you, could you please share you sessionInfo?

Thank you very much for your help

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252

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

other attached packages:
[1] cola_2.0.1 ComplexHeatmap_2.11.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.8 compiler_4.1.1 RColorBrewer_1.1-2 skmeans_0.2-14
[5] iterators_1.0.14 tools_4.1.1 mclust_5.4.9 digest_0.6.29
[9] lattice_0.20-45 clue_0.3-60 png_0.1-7 Matrix_1.4-0
[13] foreach_1.5.2 microbenchmark_1.4.9 parallel_4.1.1 xfun_0.30
[17] xml2_1.3.3 httr_1.4.2 cluster_2.1.2 knitr_1.37
[21] GlobalOptions_0.1.2 S4Vectors_0.32.3 IRanges_2.28.0 stats4_4.1.1
[25] impute_1.68.0 R6_2.5.1 GetoptLong_1.0.5 irlba_2.3.5
[29] eulerr_6.1.1 codetools_0.2-18 matrixStats_0.61.0 BiocGenerics_0.40.0
[33] shape_1.4.6 circlize_0.4.14 colorspace_2.0-3 brew_1.0-7
[37] doParallel_1.0.17 slam_0.1-50 markdown_1.1 crayon_1.5.0
[41] rjson_0.2.21

from cola.

How about restart your R session? because when you install new versions of packages, they won't be reloaded automatically.

from cola.

Already done it (I even tried to launch commands from base R instead of Rstudio). I will see if I have the time to manually load the function to better catch the issue.

from cola.

Hi everyone, today I realized the error is from the function collect_plots() where temporary png files are generated. Currently there is a problem that 1 either some variables (e.g. fun_name) cannot be properly sent into the parallel code chunk, and 2 putting png() inside the parallel code chunk makes the execution forever. I don't know why and it needs time to fix that.

Current solution is that I replaced the old parallel code with a simple lapply(). This means there won't be any parallel execution of generating figures, but at least it is safer.

from cola.