Closed SimonDMurray closed 4 years ago
It's due to your object has a rowData table with 0 column. I've added code to handle this by automatically adding the rownames as a column if 0 column is detected.
I tried to install the updated version on Rstudio using
devtools::install_github('cellgeni/sceasy', ref = "v0.0.4")
and it still only downloaded version 0.01
Downloading GitHub repo cellgeni/sceasy@v0.0.4
Skipping 2 packages not available: SingleCellExperiment, LoomExperiment
✔ checking for file ‘/private/var/folders/7d/kyg4qyys7f54fsb1ng8jbxh4000lcq/T/RtmpfrjuCb/remotes42a95514ef2f/cellgeni-sceasy-2caaff4/DESCRIPTION’ ...
─ preparing ‘sceasy’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘sceasy_0.0.1.tar.gz’
Installing package into ‘/Users/sm42/Library/R/3.6/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘sceasy’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package ‘sceasy’
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sceasy)
and so the same error still arose
The latest modifications are in master, so please try ref="master"
.
And, building ‘sceasy_0.0.1.tar.gz
has nothing to do with the actual version. It was building v0.0.4
which doesn't contain the latest fixes.
Thanks for all the help, only one function not working now. When trying to convert loom to anndata
#loom2anndata
loom_ann <- sceasy:::convertFormat('/Users/sm42/Sceasy/Test/sce_loom_data.loom', from="loom", to="anndata", outFile='/Users/sm42/Sceasy/Test/loom_ann_data.h5ad')
This error appears
Error in py_call_impl(callable, dots$args, dots$keywords) : KeyError: "Unable to open object (object 'attrs' doesn't exist)"
using this data sce_loom_data.loom.zip even though converting loom to sce works using same data
It works for me. Can you paste your relevant R and python module versions?
R version 3.6.1 on R studio and python 3.7 via anaconda
I meant things like reticulate, anndata, loompy etc.
My session info is:
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] R.methodsS3_1.7.1 sceasy_0.0.1 reticulate_1.13 hdf5r_1.3.0
[5] Seurat_3.1.1 LoomExperiment_1.2.0 rtracklayer_1.44.4 rhdf5_2.28.0
[9] SingleCellExperiment_1.6.0 SummarizedExperiment_1.14.1 DelayedArray_0.10.0 BiocParallel_1.18.1
[13] matrixStats_0.55.0 Biobase_2.44.0 GenomicRanges_1.36.1 GenomeInfoDb_1.20.0
[17] IRanges_2.18.3 S4Vectors_0.22.1 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_1.4-1 ggridges_0.5.1 XVector_0.24.0 rstudioapi_0.10
[6] leiden_0.3.1 listenv_0.7.0 npsurv_0.4-0 bit64_0.9-7 ggrepel_0.8.1
[11] codetools_0.2-16 splines_3.6.1 lsei_1.2-0 knitr_1.25 zeallot_0.1.0
[16] jsonlite_1.6 Rsamtools_2.0.2 ica_1.0-2 cluster_2.1.0 png_0.1-7
[21] R.oo_1.22.0 uwot_0.1.4 HDF5Array_1.12.2 sctransform_0.2.0 compiler_3.6.1
[26] httr_1.4.1 backports_1.1.5 assertthat_0.2.1 Matrix_1.2-17 lazyeval_0.2.2
[31] htmltools_0.4.0 tools_3.6.1 rsvd_1.0.2 igraph_1.2.4.1 gtable_0.3.0
[36] glue_1.3.1 GenomeInfoDbData_1.2.1 RANN_2.6.1 reshape2_1.4.3 dplyr_0.8.3
[41] Rcpp_1.0.2 vctrs_0.2.0 Biostrings_2.52.0 gdata_2.18.0 ape_5.3
[46] nlme_3.1-141 gbRd_0.4-11 lmtest_0.9-37 xfun_0.10 stringr_1.4.0
[51] globals_0.12.4 lifecycle_0.1.0 irlba_2.3.3 gtools_3.8.1 XML_3.98-1.20
[56] future_1.14.0 zlibbioc_1.30.0 MASS_7.3-51.4 zoo_1.8-6 scales_1.0.0
[61] RColorBrewer_1.1-2 pbapply_1.4-2 gridExtra_2.3 ggplot2_3.2.1 stringi_1.4.3
[66] caTools_1.17.1.2 bibtex_0.4.2 Rdpack_0.11-0 SDMTools_1.1-221.1 rlang_0.4.0
[71] pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-38 ROCR_1.0-7 purrr_0.3.2
[76] Rhdf5lib_1.6.1 GenomicAlignments_1.20.1 htmlwidgets_1.5.1 bit_1.1-14 cowplot_1.0.0
[81] tidyselect_0.2.5 RcppAnnoy_0.0.13 plyr_1.8.4 magrittr_1.5 R6_2.4.0
[86] gplots_3.0.1.1 pillar_1.4.2 fitdistrplus_1.0-14 survival_2.44-1.1 RCurl_1.95-4.12
[91] tsne_0.1-3 tibble_2.1.3 future.apply_1.3.0 crayon_1.3.4 KernSmooth_2.23-15
[96] plotly_4.9.0 grid_3.6.1 data.table_1.12.4 metap_1.1 digest_0.6.21
[101] tidyr_1.0.0 R.utils_2.9.0 RcppParallel_4.4.4 munsell_0.5.0 viridisLite_0.3.0
My loompy version is loompy-3.0.6 and anndata is anndata-0.6.22.post1 natsort-6.0.0
I accidentally closed the issue? Did you get my last message?
loompy-3.0.6 is not going to work. You need loompy=2.x. You might also need anndata<0.6.20.
I changed all the versions and same error still appeared. I checked my attrs version and it is 19.1.0, is this a correct version?
Turns out this is solved by pointing the r-studio copy of reticulate to use the correct conda environment (hence the correct version of loompy and anndata).
This is your SCE data
This is my sce data
When i run the line
This error is produced
i have attached my file im trying to use seur_sce_data.rds.zip