getCrispraiScores: pandas import error
Opened this issue · 4 comments
peteratfunction commented
I am trying to run getCrispraiScores using the vignette example, but run into the following error.
Docker install:
sudo docker run --rm -ti -p 8788:8787 -v $(pwd):/guide_design -e DISABLE_AUTH=true -e ROOT=true bioconductor/bioconductor_docker:devel
R:
BiocManager::install(version="devel")
BiocManager::install("crisprScore")
library(crisprScore)
results <- getCrispraiScores(tss_df=tssExampleCrispri,
sgrna_df=sgrnaExampleCrispri,
modality="CRISPRi",
fastaFile="input/hg38/fasta/hg38.fa",
chromatinFiles=c(mnase="input/hg38/bigwig/crispria_mnase_human_K562_hg38.bigWig",
dnase="input/hg38/bigwig/crispria_dnase_human_K562_hg38.bigWig",
faire="input/hg38/bigwig/crispria_faire_human_K562_hg38.bigWig"))
R output:
Traceback (most recent call last):
File "/usr/local/lib/R/site-library/crisprScore/python/crisprai/getWeissmanScores.py", line 7, in <module>
from sgRNA_learning import *
File "/usr/local/lib/R/site-library/crisprScore/python/crisprai/sgRNA_learning.py", line 8, in <module>
import pandas as pd
File "/home/rstudio/.cache/R/basilisk/1.15.3/crisprScore/1.7.2/crisprai_basilisk/lib/python2.7/site-packages/pandas/__init__.py", line 7, in <module>
from . import hashtable, tslib, lib
File "pandas/tslib.pyx", line 2839, in init pandas.tslib (pandas/tslib.c:80041)
File "pandas/algos.pyx", line 64, in init pandas.algos (pandas/algos.c:180213)
ImportError: /home/rstudio/.cache/R/basilisk/1.15.3/crisprScore/1.7.2/crisprai_basilisk/lib/python2.7/site-packages/pandas/lib.so: undefined symbol: is_float_object
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '/tmp/RtmpzFOk0q/scores.txt': No such file or directory
sessionInfo
> sessionInfo()
R Under development (unstable) (2024-01-23 r85822)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] crisprScore_1.7.2 crisprScoreData_1.7.0 ExperimentHub_2.11.1 AnnotationHub_3.11.1 BiocFileCache_2.11.1 dbplyr_2.4.0
[7] BiocGenerics_0.49.1
loaded via a namespace (and not attached):
[1] KEGGREST_1.43.0 dir.expiry_1.11.0 Biobase_2.63.0 lattice_0.22-5 vctrs_0.6.5
[6] tools_4.4.0 bitops_1.0-7 generics_0.1.3 stats4_4.4.0 curl_5.2.0
[11] parallel_4.4.0 tibble_3.2.1 fansi_1.0.6 AnnotationDbi_1.65.2 RSQLite_2.3.5
[16] blob_1.2.4 pkgconfig_2.0.3 Matrix_1.6-5 S4Vectors_0.41.3 lifecycle_1.0.4
[21] GenomeInfoDbData_1.2.11 compiler_4.4.0 stringr_1.5.1 Biostrings_2.71.2 GenomeInfoDb_1.39.5
[26] RCurl_1.98-1.14 yaml_2.3.8 pillar_1.9.0 crayon_1.5.2 cachem_1.0.8
[31] mime_0.12 basilisk_1.15.3 tidyselect_1.2.0 stringi_1.8.3 dplyr_1.1.4
[36] purrr_1.0.2 BiocVersion_3.19.1 fastmap_1.1.1 grid_4.4.0 cli_3.6.2
[41] magrittr_2.0.3 randomForest_4.7-1.1 utf8_1.2.4 withr_3.0.0 filelock_1.0.3
[46] rappdirs_0.3.3 bit64_4.0.5 XVector_0.43.1 httr_1.4.7 bit_4.0.5
[51] reticulate_1.34.0 png_0.1-8 memoise_2.0.1 IRanges_2.37.1 basilisk.utils_1.15.1
[56] rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0 DBI_1.2.1 BiocManager_1.30.22
[61] rstudioapi_0.15.0 jsonlite_1.8.8 R6_2.5.1 zlibbioc_1.49.0
Jfortin1 commented
Hi @peteratfunction, looking at it now
peteratfunction commented
Just checking up on this and to ask if there is any testing I can do to help identify the source of the problem?
jcjimbo commented
To follow up on this I'm having the same issue, is there any update?
jnhutchinson-diamondage commented
Having the same issue running the command from the dockerfile.