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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Error in eigen(delta1) : error code 1 from Lapack routine 'dsyevr' #1694

Open Gian77 opened 1 year ago

Gian77 commented 1 year ago

Hello,

I am trying to generate a pcoa form a phyloseq object and I am geeting this error below: Error in eigen(delta1) : error code 1 from Lapack routine 'dsyevr' I am running R 4.3.1 on Ubuntu 22.04, Phyloseq, vegan versions below, as well as sessionInfo(). I have libblas-dev liblapack-dev libraries installed as well as fortran. Any hint? Thnanks a lot, G.

# Calcualting PCaA ------
pcoa_ecm_jac <- 
  ordinate(physeq_ecm, method = "PCoA", distance = "jaccard", binary=TRUE)

> head(physeq_ecm@otu_table)
OTU Table:          [6 taxa and 421 samples]
                     taxa are rows
        AU_ITS_A1F AU_ITS_A1N AU_ITS_A2F AU_ITS_A2N AU_ITS_A3F AU_ITS_A3N AU_ITS_A4F AU_ITS_A4N AU_ITS_A5F AU_ITS_A5N AU_ITS_A7F AU_ITS_A7N AU_ITS_A8F AU_ITS_A8N
FOTU_4           0        715          0       2732          0        653       1589       1378          0       1236          0        606          0        926
FOTU_22          7          0        661          0        107          0          0          0          7          0        103          0          5          0
        AU_ITS_A9F AU_ITS_A9N AU_ITS_A10F AU_ITS_A10N AU_ITS_B1F AU_ITS_B1N AU_ITS_B2F AU_ITS_B2N AU_ITS_B3F AU_ITS_B3N AU_ITS_B5F AU_ITS_B5N AU_ITS_B6F AU_ITS_B6N
FOTU_4           0       1114           0         812          0        829          1         40          0        626          0        436          0       2201
FOTU_22          0          7           0           0        252          0          3         15          5          4          6         11        201          8

> head(physeq_ecm@tax_table)
Taxonomy Table:     [6 taxa by 12 taxonomic ranks]:
        Kingdom Phylum          Class            Order           Family              Genus         Species               confidence_fg     guild_fg         
FOTU_4  "Fungi" "Ascomycota"    "Pezizomycetes"  "Pezizales"     "Tuberaceae"        "Tuber"       "Tuber melanosporum"  "Highly Probable" "Ectomycorrhizal"
FOTU_22 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"    "Strophariaceae"    "Hebeloma"    "Hebeloma sp ME13_F1" "Highly Probable" "Ectomycorrhizal"
FOTU_30 "Fungi" "Ascomycota"    "Pezizomycetes"  "Pezizales"     "Pyronemataceae"    "Wilcoxina"   "Wilcoxina mikolae"   "Highly Probable" "Ectomycorrhizal"
FOTU_34 "Fungi" "Basidiomycota" "Agaricomycetes" "Boletales"     "Sclerodermataceae" "Scleroderma" "Unlcassified"        "Highly Probable" "Ectomycorrhizal"
FOTU_54 "Fungi" "Basidiomycota" "Agaricomycetes" "Agaricales"    "Strophariaceae"    "Hebeloma"    "Hebeloma mesophaeum" "Highly Probable" "Ectomycorrhizal"
FOTU_79 "Fungi" "Basidiomycota" "Agaricomycetes" "Thelephorales" "Thelephoraceae"    "Tomentella"  "Unlcassified"        "Highly Probable" "Ectomycorrhizal"

These are the other info

gian@nico-MMG:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 22.04.2 LTS
Release:    22.04
Codename:   jammy

gian@nico-MMG:~$ gfortran --version
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.

gian@nico-MMG:~$ dpkg -l | grep libatlas
ii  libatlas-base-dev:amd64                       3.10.3-12ubuntu1                        amd64        Automatically Tuned Linear Algebra Software, generic static
ii  libatlas3-base:amd64                          3.10.3-12ubuntu1                        amd64        Automatically Tuned Linear Algebra Software, generic shared

gian@nico-MMG:~$ dpkg -l | grep liblapack
ii  liblapack-dev:amd64                           3.10.0-2ubuntu1                         amd64        Library of linear algebra routines 3 - static version
ii  liblapack3:amd64                              3.10.0-2ubuntu1                         amd64        Library of linear algebra routines 3 - shared version

Then the R detailis

> packageVersion("phyloseq")
[1] ‘1.44.0’
> packageVersion("vegan")
[1] ‘2.6.4’
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so;  LAPACK version 3.8.0

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8   
 [6] LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Toronto
tzcode source: system (glibc)

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

other attached packages:
 [1] lubridate_1.9.2 forcats_1.0.0   stringr_1.5.0   dplyr_1.1.2     purrr_1.0.1     readr_2.1.4     tidyr_1.3.0     tibble_3.2.1    ggplot2_3.4.2   tidyverse_2.0.0
[11] vegan_2.6-4     lattice_0.21-8  permute_0.9-7   phyloseq_1.44.0

loaded via a namespace (and not attached):
 [1] gtable_0.3.3            rhdf5_2.44.0            Biobase_2.60.0          tzdb_0.4.0              rhdf5filters_1.12.1     vctrs_0.6.3            
 [7] tools_4.3.1             bitops_1.0-7            generics_0.1.3          biomformat_1.28.0       stats4_4.3.1            parallel_4.3.1         
[13] fansi_1.0.4             cluster_2.1.4           pkgconfig_2.0.3         Matrix_1.6-0            data.table_1.14.8       S4Vectors_0.38.1       
[19] lifecycle_1.0.3         GenomeInfoDbData_1.2.10 compiler_4.3.1          Biostrings_2.68.1       munsell_0.5.0           codetools_0.2-19       
[25] GenomeInfoDb_1.36.1     RCurl_1.98-1.12         pillar_1.9.0            crayon_1.5.2            MASS_7.3-60             iterators_1.0.14       
[31] foreach_1.5.2           nlme_3.1-162            tidyselect_1.2.0        digest_0.6.33           stringi_1.7.12          reshape2_1.4.4         
[37] splines_4.3.1           ade4_1.7-22             grid_4.3.1              colorspace_2.1-0        cli_3.6.1               magrittr_2.0.3         
[43] survival_3.5-5          utf8_1.2.3              ape_5.7-1               withr_2.5.0             scales_1.2.1            timechange_0.2.0       
[49] XVector_0.40.0          igraph_1.5.0.1          multtest_2.56.0         hms_1.1.3               IRanges_2.34.1          mgcv_1.9-0             
[55] rlang_1.1.1             Rcpp_1.0.11             glue_1.6.2              BiocGenerics_0.46.0     rstudioapi_0.15.0       jsonlite_1.8.7         
[61] R6_2.5.1                Rhdf5lib_1.22.0         plyr_1.8.8              zlibbioc_1.46.0
adrianuzkcc commented 1 month ago

Were you able to solve it?

Gian77 commented 1 month ago

Reinstalling R and R studio and avoiding automatic upgrades everything solved it for me... G.