Could not find function "run_de"

[venchi9]

Hello!

I'm not really sure what I'm doing wrong. I've successfully loaded Libra and can load the hagai_toy dataset. When I try to run the DE I get this error:

head([email protected])
orig.ident nCount_RNA nFeature_RNA replicate label
2-CCAGCGACACAACTGT SeuratProject 26 11 mouse1 lps4
2-CAGCCGACAGATTGCT SeuratProject 20 12 mouse1 lps4
2-TGCACCTCAGTTCCCT SeuratProject 17 9 mouse1 lps4
2-CGTCCATTCCTATTCA SeuratProject 14 10 mouse1 lps4
2-GATGAAACACCAGGCT SeuratProject 15 10 mouse1 lps4
2-TCAATCTCATACAGCT SeuratProject 8 5 mouse1 lps4
cell_type
2-CCAGCGACACAACTGT bone marrow derived mononuclear phagocytes
2-CAGCCGACAGATTGCT bone marrow derived mononuclear phagocytes
2-TGCACCTCAGTTCCCT bone marrow derived mononuclear phagocytes
2-CGTCCATTCCTATTCA bone marrow derived mononuclear phagocytes
2-GATGAAACACCAGGCT bone marrow derived mononuclear phagocytes
2-TCAATCTCATACAGCT bone marrow derived mononuclear phagocytes

> DE = run_de(hagai_toy)
Error in run_de(hagai_toy) : could not find function "run_de"

I've tried re-installing Libra without any luck.

[jordansquair]

I do not think this is a Libra bug. Did you library(Libra) before running the code?

[venchi9]

Yes I did and was able to look at the hagai_toy dataset. I will keep trying!

[ccasar]

I ran into this issue before when I accidentally installed the identically named Libra package from CRAN instead of installing from this github repo.

[horizon-mm]

Hi all, if you installed this package and executed update.packages() or BiocManager::install() to update all packages, it will be replaced by the CRAN Libra that has a higher version number. You'll have to uninstall the CRAN Libra and then re-install this from github.

[Jorges1000]

Can you please change the name to avoid conflicts with CRAN Libra? It was working just fine for me but after installing CRAN Libra as a dependency of another program stopped working. Had to remove CRAN Libra, but now I get this error installing neurorestore/Libra:

[1] "/shared/apps/R/4.2.0/lib/R/library"
Error: .onLoad failed in loadNamespace() for 'TMB', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/shared/apps/R/4.2.0/lib/R/library/TMB/libs/TMB.so':
/usr/lib/x86_64-linux-gnu/libblas.so.3: undefined symbol: gotoblas
Execution halted
ERROR: lazy loading failed for package ‘Libra’

• removing ‘/shared/apps/R/4.2.0/lib/R/library/Libra’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpS2W6BN/file15713dd59223/Libra_1.0.0.tar.gz’ had non-zero exit status

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: /opt/OpenBLAS/lib/libopenblas_zenp-r0.3.21.so

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

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

other attached packages:
[1] Seurat_4.1.1.9003 data.table_1.14.2 sp_1.5-0 SeuratObject_4.1.1 workflowr_1.7.0

loaded via a namespace (and not attached):
[1] plyr_1.8.7 igraph_1.3.1 lazyeval_0.2.2 splines_4.2.0
[5] listenv_0.8.0 scattermore_0.8 usethis_2.1.5 ggplot2_3.3.6
[9] digest_0.6.29 htmltools_0.5.2 fansi_1.0.3 magrittr_2.0.3
[13] memoise_2.0.1 tensor_1.5 cluster_2.1.3 ROCR_1.0-11
[17] remotes_2.4.2 globals_0.15.0 matrixStats_0.62.0 spatstat.sparse_2.1-1
[21] prettyunits_1.1.1 colorspace_2.0-3 ggrepel_0.9.1 xfun_0.31
[25] dplyr_1.0.9 callr_3.7.0 crayon_1.5.1 jsonlite_1.8.0
[29] progressr_0.10.1 spatstat.data_2.2-0 survival_3.3-1 zoo_1.8-10
[33] glue_1.6.2 polyclip_1.10-0 gtable_0.3.0 leiden_0.4.2
[37] pkgbuild_1.3.1 future.apply_1.9.0 abind_1.4-5 scales_1.2.0
[41] DBI_1.1.3 spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.9
[45] viridisLite_0.4.0 xtable_1.8-4 reticulate_1.25 spatstat.core_2.4-2
[49] htmlwidgets_1.5.4 httr_1.4.3 RColorBrewer_1.1-3 ellipsis_0.3.2
[53] ica_1.0-2 pkgconfig_2.0.3 sass_0.4.1 uwot_0.1.11
[57] deldir_1.0-6 utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.4
[61] reshape2_1.4.4 later_1.3.0 munsell_0.5.0 tools_4.2.0
[65] cachem_1.0.6 cli_3.3.0 generics_0.1.2 devtools_2.4.3
[69] ggridges_0.5.3 evaluate_0.15 stringr_1.4.0 fastmap_1.1.0
[73] yaml_2.3.5 goftest_1.2-3 processx_3.5.3 knitr_1.39
[77] fs_1.5.2 fitdistrplus_1.1-8 purrr_0.3.4 RANN_2.6.1
[81] pbapply_1.5-0 future_1.26.1 nlme_3.1-157 whisker_0.4
[85] mime_0.12 brio_1.1.3 compiler_4.2.0 rstudioapi_0.13
[89] plotly_4.10.0 curl_4.3.2 png_0.1-7 testthat_3.1.4
[93] spatstat.utils_2.3-1 tibble_3.1.7 bslib_0.3.1 stringi_1.7.6
[97] ps_1.7.0 desc_1.4.1 rgeos_0.5-9 lattice_0.20-45
[101] Matrix_1.4-1 vctrs_0.4.1 pillar_1.7.0 lifecycle_1.0.1
[105] spatstat.geom_2.4-0 lmtest_0.9-40 jquerylib_0.1.4 RcppAnnoy_0.0.19
[109] cowplot_1.1.1 irlba_2.3.5 httpuv_1.6.5 patchwork_1.1.1
[113] R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3
[117] parallelly_1.31.1 sessioninfo_1.2.2 codetools_0.2-18 MASS_7.3-57
[121] assertthat_0.2.1 pkgload_1.2.4 rprojroot_2.0.3 withr_2.5.0
[125] sctransform_0.3.4 mgcv_1.8-40 parallel_4.2.0 grid_4.2.0
[129] rpart_4.1.16 tidyr_1.2.0 rmarkdown_2.14 Rtsne_0.16
[133] git2r_0.30.1 getPass_0.2-2 shiny_1.7.1

[Jorges1000]

So, reinstalling glmmTMB resolved the problem, however to avoid further pain and allow simultaneous use of the CRAN package it would be great to change the name, perhaps "libra"?