Error 'Csparse_transpose' not found
GuillaumeSwB opened this issue · 6 comments
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.
Thanks for the bug report. Can you post the entire output of sessionInfo()?
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 `
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.
Problem solved! It was indeed an issue with the Matrix package version. Many thanks for your assistance!
would you mind testing with the released Matrix and this SpiecEasi branch:
devtools::install('zdk123/SpiecEasi', ref="patch-dep-versions")thanks
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