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drisso / SingleCellExperiment

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.
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int_colData method not found #49

Closed drighelli closed 4 years ago

drighelli commented 4 years ago

Hi,

I created a new S4 class which inherits from SCE class. With latest Bioc Devel version, when I'm trying to access the int_colData with its getter it gives me this error: Error in int_colData(sce) : could not find function "int_colData"

Using the stable version it works.

Thanks, Dario

LTLA commented 4 years ago

I can't reproduce this.

library(SingleCellExperiment)
example(SingleCellExperiment, echo=FALSE)
int_colData(sce)
## DataFrame with 100 rows and 2 columns
##                                               reducedDims     altExps
##                                               <DataFrame> <DataFrame>
## 1    0.777921:0.00431889:0.273258:...:-1.630588:-1.106927            
## 2    0.594705:0.79374440:0.101846:...:-0.523782: 0.161328            
## 3    0.881086:0.44152582:0.537429:...:-1.017354: 0.417499            
## 4    0.868095:0.87407998:0.582449:...: 0.337311: 0.243721            
## 5    0.947859:0.51485052:0.377802:...: 0.169775:-0.989959            
## ...                                                   ...         ...
## 96  0.9356636:0.668515:0.509432:...: 1.1099356:-2.7646875            
## 97  0.0471365:0.923604:0.810211:...:-0.2182588: 1.3566261            
## 98  0.7411006:0.503783:0.617955:...: 0.0509725:-0.8839501            
## 99  0.3361625:0.149487:0.244194:...:-0.7805681: 1.5371864            
## 100 0.5052326:0.842861:0.636920:...:-0.2156642: 0.0757489
Session information ``` R Under development (unstable) (2020-03-23 r78035) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS Matrix products: default BLAS: /home/luna/Software/R/trunk/lib/libRblas.so LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.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] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SingleCellExperiment_1.9.3 SummarizedExperiment_1.17.5 [3] DelayedArray_0.13.12 matrixStats_0.56.0 [5] Biobase_2.47.3 GenomicRanges_1.39.3 [7] GenomeInfoDb_1.23.17 IRanges_2.21.8 [9] S4Vectors_0.25.15 BiocGenerics_0.33.3 loaded via a namespace (and not attached): [1] lattice_0.20-41 bitops_1.0-6 grid_4.0.0 [4] zlibbioc_1.33.1 XVector_0.27.2 Matrix_1.2-18 [7] tools_4.0.0 RCurl_1.98-1.2 compiler_4.0.0 [10] BiocManager_1.30.10 GenomeInfoDbData_1.2.3 ```
drighelli commented 4 years ago

Thanks!

I don't know why, but this morning (without any change), after loading your example code, it started to work properly.

Really sorry about that!

Thanks again, Dario