yduan004
commented
2 years ago Hi Ramsey,
Thanks for your very detailed error desperation. It is very helpful! Many others are also encountering this type of error from the ExperimentHub package. I didn’t made any changes to the signatureSearch package. I guess the error was raised from the updates of ExperimentHub package. It is caused by running the eh <- ExperimentHub() code from the signatureSearch package, while users could run this code at the global environment. It is strange that the default cache location by running this code from the signatureSearch package is different from running it at RStudio/global environment. I am also debugging it, have no clue yet. Maybe you could try using the older version of the ExperimentHub package or creating the symbolic link of the old cached location to the new cached location so that the experimenthub sqlite3 file can be found?
Best, Yuzhu
On Nov 12, 2021, at 7:07 PM, Lizzy Ramsey @.***> wrote:
Hello,
I am getting an error trying to use the gess functions. lincs_gess <- gess_lincs(qsig_lincs, sortby="NCS", tau=FALSE, workers=1) Error: failed to connect to local data base database: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/37de51dbb5aa_experimenthub.sqlite3’ reason: DB file '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/37de51dbb5aa_experimenthub.sqlite3' not found
I believe this was the old default cache location for ExperimentHub and the default location changed with an update, and when I've followed the signatureSearch vignette to connect to the lincs reference database, it looks like it's stored in the new, local path
lincs EH3226 "/Users/eramsey/Library/Caches/org.R-project.R/R/ExperimentHub/608e44d025bf_3242"
My reference database path:
@.*** [1] "/Users/eramsey/Library/Caches/org.R-project.R/R/ExperimentHub/608e44d025bf_3242"
So I'm not sure why it's trying to connect to the data base at ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/37de51dbb5aa_experimenthub.sqlite3’
I also tried to build my own reference database from LINCS (following the signatureSearchData vignette) to try to avoid using ExperimentHub and it actually still ran into this error.
sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] devtools_2.4.2 usethis_2.1.3 [3] signatureSearchData_1.8.0 gprofiler2_0.2.1 [5] GeoDE_1.0 MASS_7.3-54 [7] Matrix_1.3-4 stringr_1.4.0 [9] dplyr_1.0.7 cmapR_1.6.0 [11] RSQLite_2.2.8.9000 signatureSearch_1.8.0 [13] SummarizedExperiment_1.24.0 Biobase_2.54.0 [15] GenomicRanges_1.46.0 GenomeInfoDb_1.30.0 [17] IRanges_2.28.0 S4Vectors_0.32.2 [19] MatrixGenerics_1.6.0 matrixStats_0.61.0 [21] Rcpp_1.0.7 ExperimentHub_2.2.0 [23] AnnotationHub_3.2.0 BiocGenerics_0.40.0 [25] BiocFileCache_2.2.0 dbplyr_2.1.1
https://user-images.githubusercontent.com/69320986/141603324-9e84b3b0-d971-4383-b1da-6bc7e69240e4.png Thank you for your time
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-- Yuzhu Duan, Ph.D. Candidate Genetics, Genomics and Bioinformatics Program 1207E Genomics Building University of California, Riverside Riverside, CA 92521
Tel: (951)224-7029 Email: @.***
lizzyjoan
komalsrathi
liamkelley93
jha14
Hello,
I am getting an error trying to use the gess functions. lincs_gess <- gess_lincs(qsig_lincs, sortby="NCS", tau=FALSE, workers=1) Error: failed to connect to local data base database: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/37de51dbb5aa_experimenthub.sqlite3’ reason: DB file '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/37de51dbb5aa_experimenthub.sqlite3' not found
I believe this was the old default cache location for ExperimentHub and the default location changed with an update, and when I've followed the signatureSearch vignette to connect to the lincs reference database, it looks like it's stored in the new, local path
My reference database path:
So I'm not sure why it's trying to connect to the data base at ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/37de51dbb5aa_experimenthub.sqlite3’
I also tried to build my own reference database from LINCS (following the signatureSearchData vignette) to try to avoid using ExperimentHub and it actually still ran into this error.
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] devtools_2.4.2 usethis_2.1.3
[3] signatureSearchData_1.8.0 gprofiler2_0.2.1
[5] GeoDE_1.0 MASS_7.3-54
[7] Matrix_1.3-4 stringr_1.4.0
[9] dplyr_1.0.7 cmapR_1.6.0
[11] RSQLite_2.2.8.9000 signatureSearch_1.8.0
[13] SummarizedExperiment_1.24.0 Biobase_2.54.0
[15] GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
[17] IRanges_2.28.0 S4Vectors_0.32.2
[19] MatrixGenerics_1.6.0 matrixStats_0.61.0
[21] Rcpp_1.0.7 ExperimentHub_2.2.0
[23] AnnotationHub_3.2.0 BiocGenerics_0.40.0
[25] BiocFileCache_2.2.0 dbplyr_2.1.1
Thank you for your time