getCrispraiScores: pandas import error

[peteratfunction]

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]

Hi @peteratfunction, looking at it now

[peteratfunction]

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]

To follow up on this I'm having the same issue, is there any update?

[jnhutchinson-diamondage]

Having the same issue running the command from the dockerfile.

[Jfortin1]

@jcjimbo @peteratfunction We had fixed a couple of things in crisprScore to support code that was written in Python 2.7.
The latest version (1.9.1) should work

[jcjimbo]

Many thanks for the reply and addressing the issue.

I managed to get it running initally with an error:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'query': failed to connect reason: lazy-load database '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/yaml/R/yaml.rdb' is corrupt Consider rerunning with 'localHub=TRUE'

Upon an R session refesh the error is now:

snapshotDate(): 2024-07-16 see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation loading from cache Traceback (most recent call last): File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/crisprScore/python/crisprai/getWeissmanScores.py", line 105, in <module> scores = predictWeissmanScore(tssTable, p1p2Table, sgrnaTable, libraryTable, pickleFile, fastaFile, chromatinFiles, modality, verbose) File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/crisprScore/python/crisprai/getWeissmanScores.py", line 26, in predictWeissmanScore paramTable = getParamTable(tssTable, p1p2Table, sgrnaTable, libraryTable, fastaFile, chromatinFiles, verbose) File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/crisprScore/python/crisprai/getWeissmanScores.py", line 61, in getParamTable raise Exception('Error generating parameter table.') Exception: Error generating parameter table. Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '/var/folders/vm/gdslj1hs0w1dj_wdlp589w700000gn/T//RtmpRJYKQ8/scores.txt': No such file or directory

So I am unsure how to get it running from now, do you have any suggestions?