Just to follow up on my previous post. I am able to replicate the problem in 
the problem like in the github post from 2 years ago 
(https://github.com/epurdom/clusterExperiment/issues/66 
<https://github.com/epurdom/clusterExperiment/issues/66>) only now it is not 
the SummarizedExperiment class but the SingleCellExperiment class that has the 
problem. [And I was incorrect, the problem does occur in  development version 
2018-03-22 r74446]. 

So this is actually a problem with the SingleCellExperiment package — sorry for 
the incorrect subject line.

All of the best,
Elizabeth

> > library(SingleCellExperiment)
> > SingleCellExperiment()
> class: SingleCellExperiment 
> dim: 0 0 
> metadata(0):
> assays(0):
> rownames: NULL
> rowData names(0):
> colnames: NULL
> colData names(0):
> reducedDimNames(0):
> spikeNames(0):
> > library(RNeXML)
> Loading required package: ape
> > 
> > SingleCellExperiment()
> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by ‘RNeXML’
> Found more than one class "Annotated" in cache; using the first, from 
> namespace 'S4Vectors'
> Also defined by ‘RNeXML’
> class: SingleCellExperiment 
> dim: 0 0 
> metadata(0):
> assays(0):
> rownames: NULL
> rowData names(0):
> colnames: NULL
> colData names(0):
> reducedDimNames(0):
> spikeNames(0):




> > sessionInfo()
> R Under development (unstable) (2018-03-22 r74446)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> Matrix products: default
> BLAS: 
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.5/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] parallel  stats4    stats     graphics  grDevices utils     datasets  
> methods   base     
> 
> other attached packages:
>  [1] RNeXML_2.0.8                ape_5.1                     
> SingleCellExperiment_1.1.2 
>  [4] SummarizedExperiment_1.9.16 DelayedArray_0.5.30         
> BiocParallel_1.13.3        
>  [7] matrixStats_0.53.1          Biobase_2.39.2              
> GenomicRanges_1.31.23      
> [10] GenomeInfoDb_1.15.5         IRanges_2.13.28             
> S4Vectors_0.17.41          
> [13] BiocGenerics_0.25.3        
> 
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.16           pillar_1.2.1           bindr_0.1.1            
> compiler_3.5.0        
>  [5] plyr_1.8.4             XVector_0.19.9         iterators_1.0.9        
> bitops_1.0-6          
>  [9] tools_3.5.0            zlibbioc_1.25.0        uuid_0.1-2             
> tibble_1.4.2          
> [13] jsonlite_1.5           nlme_3.1-137           lattice_0.20-35        
> pkgconfig_2.0.1       
> [17] rlang_0.2.0            Matrix_1.2-14          foreach_1.4.4          
> crul_0.5.2            
> [21] curl_3.2               bindrcpp_0.2.2         GenomeInfoDbData_1.1.0 
> dplyr_0.7.4           
> [25] httr_1.3.1             stringr_1.3.0          xml2_1.2.0             
> grid_3.5.0            
> [29] glue_1.2.0             reshape_0.8.7          data.table_1.10.4-3    
> R6_2.2.2              
> [33] XML_3.98-1.10          purrr_0.2.4            tidyr_0.8.0            
> reshape2_1.4.3        
> [37] magrittr_1.5           codetools_0.2-15       assertthat_0.2.0       
> bold_0.5.0            
> [41] taxize_0.9.3           stringi_1.1.7          lazyeval_0.2.1         
> RCurl_1.95-4.10       
> [45] zoo_1.8-1 


> On Apr 11, 2018, at 10:25 AM, Elizabeth Purdom <epur...@stat.berkeley.edu> 
> wrote:
> 
> Hello,
> 
> Our package clusterExperiment has suddenly started producing errors in the 
> bioconductor devel branch because our unit tests are failing, even though we 
> haven’t pushed any changes and they passed previously. We first noticed this 
> on April 5th. 
> 
> I believe the source of these errors likely do to calls to 
> SummarizedExperiment() creating the following messages due to conflicts in 
> ‘RNeXML’ and ’S4Vectors’ both defining class ‘Annotated':
> 
>> Found more than one class "Annotated" in cache; using the first, from 
>> namespace 'S4Vectors'
>> Also defined by ‘RNeXML’
> This is killing a vast number of our tests where we repeatedly use 
> ‘expect_silent’ calls in our unit tests and SummarizedExperiment calls 
> underlie everything.
> 
> We had this message issue two years ago 
> (https://github.com/epurdom/clusterExperiment/issues/66 
> <https://github.com/epurdom/clusterExperiment/issues/66>), when it appeared 
> to be a problem with two definitions of the ‘Annotated’ class in two packages 
> that are both dependencies of packages we call. At that time, Michael 
> Lawrence posted that he would fix the problem, and it was then fixed in later 
> versions of bioconductor/R. But it appears to be back.  I am unfortunately 
> unable to get the RNeXML package to compile from source on my computer with 
> the current Mac OS X development binary which I just downloaded (2018-04-05 
> r74542), so I haven’t been able to completely redo the code that we presented 
> in that earlier github issue to confirm it is the exact same problem. I am 
> having to rely on the error reports/logs from both Bioconductor and TravisCI 
> (e.g. 2018-04-07 r74551), where this message shows up everywhere and didn’t 
> before. Thus I’m guessing that since they are the same messages from before 
> that the source is again the call to SummarizedExperiment. 
> 
> I would note that in development version 2018-03-22 r74446, where I was able 
> to install all of the packages, I was not getting these messages. 
> 
> Thanks,
> Elizabeth Purdom


        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Reply via email to