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vjcitn / CDNMscrna

materials for single-cell RNA-seq workshop at Channing
https://vjcitn.github.io/CDNMscrna/
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error in TENxPBMCData #2

Closed mikecho95 closed 1 month ago

mikecho95 commented 2 months ago

p3k = TENxPBMCData("pbmc3k") Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name?

sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /app/R-4.3.0@i86-rhel7.0/lib64/R/lib/libRblas.so LAPACK: /app/R-4.3.0@i86-rhel7.0/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/New_York tzcode source: system (glibc)

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] TENxPBMCData_1.18.0 HDF5Array_1.28.1 rhdf5_2.44.0 DelayedArray_0.26.7
[5] S4Arrays_1.2.0 abind_1.4-5 Matrix_1.6-5 SingleCellExperiment_1.22.0 [9] SummarizedExperiment_1.30.2 Biobase_2.60.0 GenomicRanges_1.52.1 GenomeInfoDb_1.36.3
[13] IRanges_2.34.1 S4Vectors_0.38.2 BiocGenerics_0.46.0 MatrixGenerics_1.12.3
[17] matrixStats_1.3.0

vjcitn commented 2 months ago

Thanks -- that's a known problem. It has to do with using obsolete bioconductor but up-to-date dbplyr. CRAN and bioconductor are not in sync. If we use Bioconductor 3.19 (current release) this does not occur. I will indicate a solution that uses an archived dbplyr.

vjcitn commented 2 months ago

So on the channing system, you will need to use dbplyr < 2.4 ... I have dbplyr_2.3.2.tar.gz in /udd/stvjc. Just use R CMD INSTALL /udd/stvjc/dbplyr_2.3.2.tar.gz and then if that goes well, try again with the TENxPBMCData ... of course you have to restart R after installing "new" package. Find the source at https://cran.r-project.org/src/contrib/Archive/dbplyr/ ... all CRAN packages have an Archived versions link towards the bottom of CRAN package page

vjcitn commented 2 months ago

One of the virtues of using up-to-date Bioconductor is that at least at the time of the release, all packages work together with the contemporaneous CRAN packages. But the CRAN packages can introduce breaking changes at any time, whereas breaking changes to bioconductor packages can only arise after six months of deprecation warning. So sometimes we need to back down a CRAN package, or really adapt Bioconductor code to changes in CRAN dependencies, in a "non-breaking" way.