Error 'Csparse_transpose' not found

[GuillaumeSwB]

Hi ! I've some trouble while running the example code provided to work with phyloseq object.

Thank you for your assistance,

Best,

Guillaume

library(phyloseq)
## Load round 2 of American gut project
data('amgut2.filt.phy')
se.mb.amgut2 <- spiec.easi(amgut2.filt.phy, method='mb', lambda.min.ratio=1e-2,
+                            nlambda=20, pulsar.params=list(rep.num=50))
Applying data transformations...
Selecting model with pulsar using stars...
Fitting final estimate with mb...
done
ig2.mb <- adj2igraph(getRefit(se.mb.amgut2),  vertex.attr=list(name=taxa_names(amgut2.filt.phy)))
Error in t(object) : object 'Csparse_transpose' not found

Edit1: Here are some details about my build:

> version
               _                           
platform       x86_64-apple-darwin20       
arch           x86_64                      
os             darwin20                    
system         x86_64, darwin20            
status                                     
major          4                           
minor          3.1                         
year           2023                        
month          06                          
day            16                          
svn rev        84548                       
language       R                           
version.string R version 4.3.1 (2023-06-16)
nickname       Beagle Scouts   

Edit2: After updating all packages, the error message changed to: Error in t(object) : invalid 'lazy' to R_sparse_transpose()

The same error occurs with the command "symBeta" of SpiecEasi.

[zdk123]

Thanks for the bug report. Can you post the entire output of sessionInfo()?

[GuillaumeSwB]

Sure

`

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Santiago tzcode source: internal

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

other attached packages: [1] SpiecEasi_1.1.2 phyloseq_1.44.0

loaded via a namespace (and not attached): [1] shape_1.4.6 gtable_0.3.4 ggplot2_3.4.3 rhdf5_2.44.0
[5] Biobase_2.60.0 lattice_0.21-8 rhdf5filters_1.12.1 vctrs_0.6.3
[9] tools_4.3.1 bitops_1.0-7 generics_0.1.3 biomformat_1.28.0
[13] stats4_4.3.1 parallel_4.3.1 tibble_3.2.1 fansi_1.0.4
[17] cluster_2.1.4 pkgconfig_2.0.3 Matrix_1.6-2 huge_1.3.5
[21] data.table_1.14.8 S4Vectors_0.38.1 lifecycle_1.0.3 GenomeInfoDbData_1.2.10 [25] compiler_4.3.1 stringr_1.5.0 Biostrings_2.68.1 munsell_0.5.0
[29] codetools_0.2-19 permute_0.9-7 GenomeInfoDb_1.36.3 glmnet_4.1-8
[33] RCurl_1.98-1.12 pillar_1.9.0 crayon_1.5.2 MASS_7.3-60
[37] vegan_2.6-4 iterators_1.0.14 foreach_1.5.2 nlme_3.1-163
[41] tidyselect_1.2.0 digest_0.6.33 stringi_1.7.12 dplyr_1.1.3
[45] reshape2_1.4.4 splines_4.3.1 ade4_1.7-22 grid_4.3.1
[49] colorspace_2.1-0 cli_3.6.1 magrittr_2.0.3 survival_3.5-7
[53] utf8_1.2.3 ape_5.7-1 scales_1.2.1 XVector_0.40.0
[57] igraph_1.5.1.9006 multtest_2.56.0 pulsar_0.3.10 VGAM_1.1-9
[61] IRanges_2.34.1 mgcv_1.9-0 rlang_1.1.1 Rcpp_1.0.11
[65] glue_1.6.2 BiocGenerics_0.46.0 rstudioapi_0.15.0 jsonlite_1.8.7
[69] R6_2.5.1 Rhdf5lib_1.22.1 plyr_1.8.8 zlibbioc_1.46.0 `

[zdk123]

Matrix 1.6-2 (which isn't officially released yet) has some changes that are not handled in pulsar. I'm planning to push a patch for those soon, but down grading Matrix to 1.5 should also work for now.

[GuillaumeSwB]

Problem solved! It was indeed an issue with the Matrix package version. Many thanks for your assistance!

[zdk123]

would you mind testing with the released Matrix and this SpiecEasi branch:

devtools::install('zdk123/SpiecEasi', ref="patch-dep-versions")

thanks

[BakDK]

A bit late, but tried testing the above with the update but it does not fix it for me. I get the same error as before.

> data('amgut2.filt.phy')
> se.mb.amgut2 <- spiec.easi(amgut2.filt.phy, method='mb', lambda.min.ratio=1e-2,
+                            nlambda=20, pulsar.params=list(rep.num=50))
Applying data transformations...
Selecting model with pulsar using stars...
Fitting final estimate with mb...
done
> ig2.mb <- adj2igraph(getRefit(se.mb.amgut2),  vertex.attr=list(name=taxa_names(amgut2.filt.phy)))
Error in h(simpleError(msg, call)) : 
  fejl under evaluering af argument 'current' under valg af metode for funktion 'all.equal': object 'Csparse_transpose' not found 

> sessionInfo() R version 4.2.1 Patched (2022-06-29 r82537 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=Danish_Denmark.utf8 LC_CTYPE=Danish_Denmark.utf8 LC_MONETARY=Danish_Denmark.utf8 LC_NUMERIC=C
[5] LC_TIME=Danish_Denmark.utf8

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

other attached packages: [1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[9] ggplot2_3.5.0 tidyverse_2.0.0 phyloseq_1.40.0 SpiecEasi_1.1.3 devtools_2.4.5 usethis_2.2.3

loaded via a namespace (and not attached): [1] nlme_3.1-164 bitops_1.0-7 fs_1.6.3 GenomeInfoDb_1.32.4 tools_4.2.1 profvis_0.3.8
[7] utf8_1.2.4 R6_2.5.1 vegan_2.6-4 DBI_1.2.2 mgcv_1.9-1 BiocGenerics_0.42.0
[13] colorspace_2.1-0 permute_0.9-7 rhdf5filters_1.8.0 ade4_1.7-22 withr_3.0.0 urlchecker_1.0.1
[19] tidyselect_1.2.0 processx_3.8.3 curl_5.2.0 compiler_4.2.1 glmnet_4.1-8 cli_3.6.2
[25] Biobase_2.56.0 desc_1.4.3 scales_1.3.0 callr_3.7.5 digest_0.6.34 XVector_0.36.0
[31] pkgconfig_2.0.3 htmltools_0.5.7 sessioninfo_1.2.2 fastmap_1.1.1 htmlwidgets_1.6.4 rlang_1.1.3
[37] rstudioapi_0.15.0 huge_1.3.5 VGAM_1.1-11 shiny_1.8.0 shape_1.4.6.1 generics_0.1.3
[43] jsonlite_1.8.8 RCurl_1.98-1.14 magrittr_2.0.3 GenomeInfoDbData_1.2.8 biomformat_1.24.0 Matrix_1.6-5
[49] Rcpp_1.0.12 munsell_0.5.0 S4Vectors_0.34.0 Rhdf5lib_1.18.2 fansi_1.0.6 ape_5.7-1
[55] lifecycle_1.0.4 stringi_1.8.3 MASS_7.3-60.0.1 zlibbioc_1.42.0 rhdf5_2.40.0 pkgbuild_1.4.3
[61] plyr_1.8.9 grid_4.2.1 parallel_4.2.1 promises_1.2.1 crayon_1.5.2 miniUI_0.1.1.1
[67] lattice_0.22-5 Biostrings_2.64.1 splines_4.2.1 multtest_2.52.0 hms_1.1.3 ps_1.7.6
[73] pillar_1.9.0 igraph_2.0.3 pulsar_0.3.11 reshape2_1.4.4 codetools_0.2-19 stats4_4.2.1
[79] pkgload_1.3.4 glue_1.7.0 data.table_1.15.0 remotes_2.4.2.1 tzdb_0.4.0 vctrs_0.6.5
[85] httpuv_1.6.14 foreach_1.5.2 gtable_0.3.4 cachem_1.0.8 mime_0.12 xtable_1.8-4
[91] later_1.3.2 survival_3.5-8 iterators_1.0.14 memoise_2.0.1 IRanges_2.30.1 cluster_2.1.6
[97] timechange_0.3.0 ellipsis_0.3.2