object ‘markvario’ is not exported by 'namespace:spatstat'

[yimingsun12138]

Hello, I report an install bug here. I installed the latest version of 'spatsat' released at 2021-03-13, and when I try to install the seurat-dist ,I got the error report:

object ‘markvario’ is not exported by 'namespace:spatstat'

So, I installed the older version of spatsat-1.64-1, and problem solved.

I think the seurat-dist may be not compatible with the latest spatsat and need some update. Thank you for your amazing job.

[Kedde92]

Hello yimingsun12138

Could you be so kind as to tell me how I can install the older version (spatsat-1.64-1).
I am quite new to R..

Best regards
Kristian

[yimingsun12138]

Hello yimingsun12138

Could you be so kind as to tell me how I can install the older version (spatsat-1.64-1).
I am quite new to R..

Best regards
Kristian

Hello Kedde92

You can refer to this page

or you can simply execute the code below in R and ignore the update recommendation for now

install.packages('https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz', repos=NULL,type="source")

[AleksZakirov]

Hello yimingsun12138
Could you be so kind as to tell me how I can install the older version (spatsat-1.64-1).
I am quite new to R..
Best regards
Kristian

Hello Kedde92

You can refer to this page

or you can simply execute the code below in R and ignore the update recommendation for now

install.packages('https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz', repos=NULL,type="source")

Unfortunately, this did not work for me. Still experiencing the same issue. Can somebody suggest alternative solutions?

Thanks!

[ChelseaCHENX]

Hey guys - I was encountered with the same issue at the moment
I don't know what errors you've got, but install.packages('https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz', repos=NULL,type="source", INSTALL_opts = "--no-lock") works for me

[rLannes]

Solution does not works for me.

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.10

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

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

loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-0 deldir_0.2-10 ellipsis_0.3.1 ggridges_0.5.3
[6] rprojroot_2.0.2 fs_1.5.0 rstudioapi_0.13 spatstat.data_2.0-0 leiden_0.3.7
[11] listenv_0.8.0 remotes_2.2.0 ggrepel_0.9.1 fansi_0.4.2 codetools_0.2-16
[16] splines_4.0.2 cachem_1.0.4 pkgload_1.2.0 polyclip_1.10-0 jsonlite_1.7.2
[21] ica_1.0-2 cluster_2.1.0 png_0.1-7 spatstat.linnet_1.65-3 shiny_1.6.0
[26] sctransform_0.3.2 spatstat.sparse_1.2-1 BiocManager_1.30.10 compiler_4.0.2 httr_1.4.2
[31] assertthat_0.2.1 SeuratObject_4.0.0 Matrix_1.2-18 fastmap_1.1.0 lazyeval_0.2.2
[36] cli_2.3.1 later_1.1.0.1 prettyunits_1.1.1 htmltools_0.5.1.1 tools_4.0.2
[41] igraph_1.2.6 gtable_0.3.0 glue_1.4.2 RANN_2.6.1 reshape2_1.4.4
[46] dplyr_1.0.5 Rcpp_1.0.6 spatstat_1.64-1 scattermore_0.7 vctrs_0.3.6
[51] nlme_3.1-149 lmtest_0.9-38 stringr_1.4.0 ps_1.6.0 globals_0.14.0
[56] testthat_3.0.2 mime_0.10 miniUI_0.1.1.1 lifecycle_1.0.0 irlba_2.3.3
[61] devtools_2.3.2 goftest_1.2-2 future_1.21.0 MASS_7.3-52 zoo_1.8-9
[66] scales_1.1.1 spatstat.core_1.65-5 promises_1.2.0.1 spatstat.utils_2.0-0 parallel_4.0.2
[71] RColorBrewer_1.1-2 curl_4.3 memoise_2.0.0 reticulate_1.18 pbapply_1.4-3
[76] gridExtra_2.3 ggplot2_3.3.3 rpart_4.1-15 stringi_1.5.3 desc_1.3.0
[81] pkgbuild_1.2.0 rlang_0.4.10 pkgconfig_2.0.3 matrixStats_0.58.0 lattice_0.20-41
[86] ROCR_1.0-11 purrr_0.3.4 tensor_1.5 patchwork_1.1.1 htmlwidgets_1.5.3
[91] processx_3.4.5 cowplot_1.1.1 tidyselect_1.1.0 parallelly_1.24.0 RcppAnnoy_0.0.18
[96] plyr_1.8.6 magrittr_2.0.1 R6_2.5.0 generics_0.1.0 DBI_1.1.1
[101] withr_2.4.1 pillar_1.5.1 mgcv_1.8-32 fitdistrplus_1.1-3 survival_3.2-3
[106] abind_1.4-5 tibble_3.1.0 future.apply_1.7.0 crayon_1.4.1 KernSmooth_2.23-17
[111] utf8_1.2.1 spatstat.geom_1.65-5 plotly_4.9.3 usethis_2.0.1 grid_4.0.2
[116] data.table_1.14.0 callr_3.5.1 digest_0.6.27 xtable_1.8-4 tidyr_1.1.3
[121] httpuv_1.5.5 munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1

[abbaslab]

Similar issue, see solution below. I run install.packages("Seurat"), it runs within 5 seconds without showing errors (so I don't think it actually worked as it only took 5 seconds to install)
then when I try to run the library("Seurat"), I get

library(Seurat)
Error: package or namespace load failed for ‘Seurat’:
object ‘markvario’ is not exported by 'namespace:spatstat'

Then, I tried:
remove.packages("Seurat", lib="/Library/Frameworks/R.framework/Versions/4.0/Resources/library/") #path to your library
remove.packages("SeuratObject", lib="/Library/Frameworks/R.framework/Versions/4.0/Resources/library/") #path to your library
remove.packages("spatstat", lib="/Library/Frameworks/R.framework/Versions/4.0/Resources/library/") #path to your library
install.packages("Seurat") ### << When it asks for compilation, when I select "Yes", it, the installation fails. but if I select "No", it worked just fine.
library("Seurat")

[mojaveazure]

Hi all,

The {spatstat} package made updates that moved some of their functions to other packages. This broke {Seurat}, which in turn, breaks {SeuratDisk}. We are working on a fix for {Seurat} to solve this; in the mean time, you should be able to downgrade your {spatstat} installation with

remotes::install_version("spatstat", version = "1.64-1")

Once {Seurat} is updated to support the latest version of {spatstat}, this issue should be resolved.