Comments (8)
I am happy to hear you solved your problem. If you decide to try msigdbr again, try reinstalling it first.
from msigdbr.
Btw on my local machine msigdbr works fine! It was very useful!
I only have trouble in using it on a server machine. The package itself is great!
from msigdbr.
The error looks like it might be related to the tidyselect package.
Can you post the output of sessionInfo()
?
from msigdbr.
sure, thank you so much!
R version 4.2.0 (2022-04-22)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /home/appierdo/.conda/envs/r/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] msigdbr_7.5.1 msigdb_1.4.0 data.table_1.14.4
[4] GSEABase_1.58.0 graph_1.74.0 annotate_1.74.0
[7] XML_3.99-0.13 AnnotationDbi_1.58.0 IRanges_2.30.1
[10] S4Vectors_0.34.0 Biobase_2.56.0 BiocGenerics_0.42.0
[13] GSVA_1.44.5
loaded via a namespace (and not attached):
[1] MatrixGenerics_1.8.1 httr_1.4.4
[3] BiocSingular_1.12.0 bit64_4.0.5
[5] jsonlite_1.8.0 DelayedMatrixStats_1.18.2
[7] assertthat_0.2.1 blob_1.2.3
[9] GenomeInfoDbData_1.2.8 pillar_1.7.0
[11] RSQLite_2.2.18 lattice_0.20-45
[13] glue_1.6.2 beachmat_2.12.0
[15] uuid_1.1-0 digest_0.6.29
[17] GenomicRanges_1.48.0 XVector_0.36.0
[19] htmltools_0.5.4 Matrix_1.5-1
[21] pkgconfig_2.0.3 babelgene_22.9
[23] zlibbioc_1.42.0 xtable_1.8-4
[25] ScaledMatrix_1.4.1 HDF5Array_1.24.2
[27] BiocParallel_1.30.4 tibble_3.1.8
[29] KEGGREST_1.36.3 generics_0.1.3
[31] ellipsis_0.3.2 withr_2.5.0
[33] cachem_1.0.6 SummarizedExperiment_1.26.1
[35] repr_1.1.4 cli_3.6.0
[37] magrittr_2.0.3 crayon_1.5.1
[39] memoise_2.0.1 evaluate_0.15
[41] fansi_1.0.3 tools_4.2.0
[43] lifecycle_1.0.1 matrixStats_0.63.0
[45] Rhdf5lib_1.18.2 DelayedArray_0.22.0
[47] irlba_2.3.5.1 Biostrings_2.64.1
[49] compiler_4.2.0 GenomeInfoDb_1.32.4
[51] rsvd_1.0.5 rlang_1.0.6
[53] rhdf5_2.40.0 grid_4.2.0
[55] RCurl_1.98-1.9 pbdZMQ_0.3-7
[57] IRkernel_1.3.1.9000 rhdf5filters_1.8.0
[59] SingleCellExperiment_1.18.1 bitops_1.0-7
[61] base64enc_0.1-3 codetools_0.2-18
[63] DBI_1.1.3 R6_2.5.1
[65] dplyr_1.0.10 fastmap_1.1.0
[67] bit_4.0.4 utf8_1.2.2
[69] parallel_4.2.0 IRdisplay_1.1
[71] Rcpp_1.0.9 vctrs_0.4.1
[73] png_0.1-7 tidyselect_1.2.0
[75] sparseMatrixStats_1.8.0
from msigdbr.
You may have a conflict due to some of the loaded packages. Can you try using msigdbr in a clean environment where only msigdbr is loaded?
from msigdbr.
same error :(
here follows the output of sessionInfo()
I'm trying to detach also the loaded via a namespace (and not attached) packages. Thank you for the suggestion!
R version 4.2.0 (2022-04-22)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /home/appierdo/.conda/envs/r/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8
[7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] msigdbr_7.5.1
loaded via a namespace (and not attached):
[1] magrittr_2.0.3 tidyselect_1.2.0 uuid_1.1-0
[4] babelgene_22.9 R6_2.5.1 rlang_1.0.6
[7] fastmap_1.1.0 fansi_1.0.3 dplyr_1.0.10
[10] tools_4.2.0 utf8_1.2.2 DBI_1.1.3
[13] cli_3.6.0 withr_2.5.0 htmltools_0.5.4
[16] ellipsis_0.3.2 assertthat_0.2.1 digest_0.6.29
[19] tibble_3.1.8 lifecycle_1.0.1 crayon_1.5.1
[22] IRdisplay_1.1 repr_1.1.4 base64enc_0.1-3
[25] vctrs_0.4.1 IRkernel_1.3.1.9000 glue_1.6.2
[28] evaluate_0.15 pbdZMQ_0.3-7 compiler_4.2.0
[31] pillar_1.7.0 generics_0.1.3 jsonlite_1.8.0
[34] pkgconfig_2.0.3
from msigdbr.
You still have some extra packages that are loaded, such as IRdisplay and DBI.
For comparison, this is what I am seeing:
> library(msigdbr)
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.2
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] msigdbr_7.5.1
loaded via a namespace (and not attached):
[1] fansi_1.0.4 utf8_1.2.3 dplyr_1.1.0 R6_2.5.1 lifecycle_1.0.3
[6] magrittr_2.0.3 pillar_1.8.1 rlang_1.0.6 cli_3.6.0 rstudioapi_0.14
[11] generics_0.1.3 vctrs_0.5.2 tools_4.2.2 glue_1.6.2 compiler_4.2.2
[16] pkgconfig_2.0.3 babelgene_22.9 tidyselect_1.2.0 tibble_3.1.8
from msigdbr.
I really appreciated the prompt help, at the moment I can't figure out how to solve the problem, but I've managed to obtain what I needed in a different way. I'm going to close the issue for now. Thanks again!
from msigdbr.
Related Issues (20)
- `unused argument (.data$species_name == species)` error HOT 3
- enricher result is different from msigDB web "investigate Gene Sets" HOT 2
- Ensembl Gene IDs HOT 3
- Skip 7.3 CRAN release and go straight to 7.4(?) HOT 1
- MSigDB 7.4 HOT 4
- Methodology details, and `write.gmt` helper functions? HOT 3
- Add shorter GO descriptions? HOT 3
- msigdbr package, category C2, subcategory CP HOT 4
- number of gene sets HOT 4
- First release of Mouse MSigDB (v2022.1.Mm) HOT 1
- Save the 'entrez_gene' columns in character mode HOT 3
- Problem with dyplr dependency (I think) HOT 1
- Inconsistent gene set contents with MSigDB HOT 6
- Run KEGG in Seurat object HOT 1
- Accessing Mouse MSigDB Collections HOT 1
- 2023 update? HOT 5
- Help with checking a pathway in msigdb.
- C2:CGP pathways being labelled as C2:CP pathways HOT 1
- misgdbr for yeast HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from msigdbr.