Open alex-d13 opened 3 years ago
I am suspecting, that some other package is messing SpiecEasi up, do you maybe have an idea, which one it could be? My session-info:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices datasets utils methods base
other attached packages:
[1] SpiecEasi_1.0.7 DECIPHER_2.14.0 RSQLite_2.2.4 proxy_0.4-25 renv_0.13.1
[6] shinydashboardPlus_2.0.0 shinydashboard_0.7.1 shinyWidgets_0.6.0 fontawesome_0.1.0 Biostrings_2.54.0
[11] XVector_0.26.0 IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0 dada2_1.14.1
[16] waiter_0.2.0 biomformat_1.14.0 mdine_1.0.2 MLmetrics_1.1.1 MLeval_0.3
[21] shinyjs_2.0.0 gbm_2.1.8 ranger_0.12.1 caret_6.0-86 NbClust_3.0
[26] phyloseq_1.30.0 Matrix_1.3-2 igraph_1.2.6 themetagenomics_1.0.2 Rcpp_1.0.6
[31] umap_0.2.7.0 tidyr_1.1.3 textshape_1.7.1 shiny_1.6.0 Rtsne_0.15
[36] reshape2_1.4.4 RColorBrewer_1.1-2 phangorn_2.6.2 klaR_0.6-15 MASS_7.3-53.1
[41] networkD3_0.4 heatmaply_1.2.1 viridis_0.5.1 viridisLite_0.3.0 plotly_4.9.3
[46] ggplot2_3.3.3 GUniFrac_1.1 matrixStats_0.58.0 ape_5.4-1 vegan_2.5-7
[51] lattice_0.20-41 permute_0.9-5 fpc_2.2-9 DT_0.17 cluster_2.1.1
[56] data.table_1.14.0 ade4_1.7-16
loaded via a namespace (and not attached):
[1] utf8_1.2.1 questionr_0.7.4 reticulate_1.18 tidyselect_1.1.0 lme4_1.1-26
[6] htmlwidgets_1.5.3 BiocParallel_1.20.1 grid_3.6.3 TSP_1.1-10 combinat_0.0-8
[11] pROC_1.17.0.1 munsell_0.5.0 codetools_0.2-18 statmod_1.4.35 miniUI_0.1.1.1
[16] withr_2.4.1 colorspace_2.0-0 Biobase_2.46.0 highr_0.8 rstudioapi_0.13
[21] robustbase_0.93-7 huge_1.3.4.1 rstan_2.21.2 GenomeInfoDbData_1.2.2 hwriter_1.3.2
[26] bit64_4.0.5 rhdf5_2.30.1 vctrs_0.3.6 generics_0.1.0 ipred_0.9-11
[31] GenomeInfoDb_1.22.1 diptest_0.75-7 R6_2.5.0 VGAM_1.1-5 pulsar_0.3.7
[36] seriation_1.2-9 flexmix_2.3-17 cachem_1.0.4 DelayedArray_0.12.3 bitops_1.0-6
[41] assertthat_0.2.1 promises_1.2.0.1 scales_1.1.1 nnet_7.3-15 gtable_0.3.0
[46] processx_3.4.5 timeDate_3043.102 rlang_0.4.10 splines_3.6.3 lazyeval_0.2.2
[51] ModelMetrics_1.2.2.2 inline_0.3.17 BiocManager_1.30.10 httpuv_1.5.5 tools_3.6.3
[56] lava_1.6.9 ellipsis_0.3.1 jquerylib_0.1.3 plyr_1.8.6 progress_1.2.2
[61] zlibbioc_1.32.0 RCurl_1.98-1.3 purrr_0.3.4 ps_1.6.0 prettyunits_1.1.1
[66] rpart_4.1-15 openssl_1.4.3 SummarizedExperiment_1.16.1 haven_2.3.1 magrittr_2.0.1
[71] RSpectra_0.16-0 hms_1.0.0 mime_0.10 xtable_1.8-4 jpeg_0.1-8.1
[76] mclust_5.4.7 rstantools_2.1.1 gridExtra_2.3 compiler_3.6.3 tibble_3.1.0
[81] V8_3.4.0 crayon_1.4.1 minqa_1.2.4 StanHeaders_2.21.0-7 htmltools_0.5.1.1
[86] mgcv_1.8-34 later_1.1.0.1 RcppParallel_5.0.3 lubridate_1.7.10 DBI_1.1.1
[91] boot_1.3-27 ShortRead_1.44.3 cli_2.3.1 quadprog_1.5-8 gower_0.2.2
[96] GenomicRanges_1.38.0 forcats_0.5.1 pkgconfig_2.0.3 GenomicAlignments_1.22.1 registry_0.5-1
[101] recipes_0.1.15 foreach_1.5.1 lda_1.4.2 bslib_0.2.4 multtest_2.42.0
[106] webshot_0.5.2 prodlim_2019.11.13 stringr_1.4.0 callr_3.5.1 digest_0.6.27
[111] fastmatch_1.1-0 dendextend_1.14.0 curl_4.3 kernlab_0.9-29 Rsamtools_2.2.3
[116] modeltools_0.2-23 nloptr_1.2.2.2 lifecycle_1.0.0 nlme_3.1-152 jsonlite_1.7.2
[121] Rhdf5lib_1.8.0 askpass_1.1 fansi_0.4.2 labelled_2.8.0 pillar_1.5.1
[126] loo_2.4.1 fastmap_1.1.0 httr_1.4.2 DEoptimR_1.0-8 pkgbuild_1.2.0
[131] survival_3.2-10 glue_1.4.2 png_0.1-7 prabclus_2.3-2 iterators_1.0.13
[136] bit_4.0.4 sass_0.3.1 class_7.3-18 stringi_1.5.3 blob_1.2.1
[141] memoise_2.0.0 latticeExtra_0.6-29 dplyr_1.0.5
Thanks for the report. I did some googling and this "bad error message" may be a result of a too-long error being returned from an assertion.
I do see from your package list that your SpiecEasi version is slightly out of date (we're up to 1.1.0 now). You can try upgrading that, but the neighborhood selection code hasn't been touched in a while so I'd be surprised if that made a difference.
If you could provide a reproducible example (if you would be willing to share private data via email) that would be much appreciated.
Hi, thanks for the quick response.
I found the issue already, it was the renv package. When I unload it with detach("package:renv")
, SpiecEasi works just fine again.
It probably messes up some base functions, that you are using.
great, thanks for the fix. I'll update the issue title and try to reproduce with the test data.
I was able to reproduce the issue by loading renv before running the tests. It looks like we're inadvertently dispatching to renv::update
instead of stats::update
when that package is loaded.
This may be related to #47.
Hi, I am getting a strange error message, when I try to run SpiecEasi:
spiec.easi(phylo, method='mb', lambda.min.ratio=1e-2, nlambda=20, pulsar.params=list(rep.num=50))
Applying data transformations...
Error in stop(err) : bad error message
My phyloseq-object looks like this:
Do you have an idea, what is going on here?