standardChromosomes() function not found but its guide yes.
Hi, I'm having troubles working in R (loaded via conda env). I installed all the packages required via conda but when I tried to use the function standardChromosomes() from the package GenomeInfodb I'm just able to recall the guide with ?standardChromosomes() but not using the function itself (it says "function not found").
How it is possible? Thanks
Francesca
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /hpcnfs/home/ieo5212/.conda/envs/R/lib/libopenblasp-r0.3.18.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Signac_1.7.0
loaded via a namespace (and not attached):
[1] SeuratObject_4.0.4 Rcpp_1.0.8 lattice_0.20-45
[4] tidyr_1.1.4 listenv_0.8.0 Rsamtools_2.10.0
[7] Biostrings_2.62.0 assertthat_0.2.1 digest_0.6.29
[10] utf8_1.2.2 parallelly_1.30.0 IRdisplay_1.1
[13] R6_2.5.1 GenomeInfoDb_1.30.0 repr_1.1.4
[16] stats4_4.1.3 evaluate_0.14 ggplot2_3.3.5
[19] pillar_1.6.4 zlibbioc_1.40.0 rlang_1.0.2
[22] uuid_1.0-3 irlba_2.3.5 data.table_1.14.2
[25] S4Vectors_0.32.3 Matrix_1.4-0 BiocParallel_1.28.3
[28] RCurl_1.98-1.6 munsell_0.5.0 compiler_4.1.3
[31] pkgconfig_2.0.3 BiocGenerics_0.40.0 base64enc_0.1-3
[34] globals_0.14.0 htmltools_0.5.2 tidyselect_1.1.1
[37] tibble_3.1.6 GenomeInfoDbData_1.2.7 IRanges_2.28.0
[40] codetools_0.2-18 RcppRoll_0.3.0 fansi_1.0.2
[43] future_1.23.0 crayon_1.4.2 dplyr_1.0.7
[46] bitops_1.0-7 grid_4.1.3 jsonlite_1.8.0
[49] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
[52] magrittr_2.0.1 scales_1.1.1 stringi_1.7.6
[55] pbapply_1.5-0 future.apply_1.8.1 cli_3.1.1
[58] XVector_0.34.0 ellipsis_0.3.2 generics_0.1.1
[61] vctrs_0.3.8 fastmatch_1.1-3 IRkernel_1.3
[64] tools_4.1.3 glue_1.6.1 purrr_0.3.4
[67] parallel_4.1.3 fastmap_1.1.0 colorspace_2.0-2
[70] GenomicRanges_1.46.1 pbdZMQ_0.3-6 patchwork_1.1.1
• 1,782 views
•
link
0 answers
No answers yet.
Log in to answer this question.
It is very strange. I'm able to run
But not
I'm able to do it for other packages, but in this case it says package not found
Try reinstalling the package.
In the end I created a new env conda and I installed everything again. Very boring solution but the only one that solved every problem