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coregenomics / kmap

Generate mappable regions of the genome for a given K-mer length.
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Cannot install Bioconductor packages after loading QuasR #5

Open omsai opened 7 years ago

omsai commented 7 years ago

Trying to install a missing genome fails because QuasR loads BiocInstaller!?

 > library(kmap)
 > mappable("hg38")
 Error in .stopOnAvailablePkg(genome) :
   BSgenome.Hsapiens.UCSC.hg38 package is not currently installed.
   You first need to install it, which you can do with:
       library(BiocInstaller)
       biocLite("BSgenome.Hsapiens.UCSC.hg38")
 > BiocInstaller::biocLite("BSgenome.Hsapiens.UCSC.hg38")
 Error: failed to update BiocInstaller:
     namespace ‘BiocInstaller’ is imported by ‘QuasR’ so cannot be unloaded
 >

Reproducible in a fresh R session:

> library(QuasR)
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rbowtie
> BiocInstaller::biocLite("BSgenome.Hsapiens.UCSC.hg38")
Error: failed to update BiocInstaller:
    namespace ‘BiocInstaller’ is imported by ‘QuasR’ so cannot be unloaded
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] QuasR_1.16.0         Rbowtie_1.16.0       GenomicRanges_1.28.4
[4] GenomeInfoDb_1.12.2  IRanges_2.10.2       S4Vectors_0.14.3    
[7] BiocGenerics_0.22.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               RColorBrewer_1.1-2        
 [3] BiocInstaller_1.26.0       compiler_3.4.1            
 [5] XVector_0.16.0             GenomicFeatures_1.28.4    
 [7] bitops_1.0-6               GenomicFiles_1.12.0       
 [9] tools_3.4.1                zlibbioc_1.22.0           
[11] biomaRt_2.32.1             digest_0.6.12             
[13] bit_1.1-12                 BSgenome_1.44.1           
[15] RSQLite_2.0                memoise_1.1.0             
[17] tibble_1.3.3               lattice_0.20-35           
[19] rlang_0.1.1                Matrix_1.2-11             
[21] DelayedArray_0.2.7         DBI_0.7                   
[23] GenomeInfoDbData_0.99.0    hwriter_1.3.2             
[25] rtracklayer_1.36.4         Biostrings_2.44.2         
[27] bit64_0.9-7                grid_3.4.1                
[29] Biobase_2.36.2             AnnotationDbi_1.38.2      
[31] XML_3.98-1.9               BiocParallel_1.10.1       
[33] latticeExtra_0.6-28        blob_1.1.0                
[35] Rsamtools_1.28.0           matrixStats_0.52.2        
[37] GenomicAlignments_1.12.2   ShortRead_1.34.0          
[39] SummarizedExperiment_1.6.3 RCurl_1.95-4.8            
[41] VariantAnnotation_1.22.3  
>
omsai commented 7 years ago

Persists with R daily build:

> suppressPackageStartupMessages(library(QuasR))
> BiocInstaller::biocLite("BSgenome.Hsapiens.UCSC.hg38")
Error: failed to update BiocInstaller:
    namespace ‘BiocInstaller’ is imported by ‘QuasR’ so cannot be unloaded
> sessionInfo()
R Under development (unstable) (2017-08-01 r73012)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-08-01-jyjbn6hodegfxzvg6aojsdu7fmrdzi3y/rlib/R/lib/libRblas.so
LAPACK: /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-08-01-jyjbn6hodegfxzvg6aojsdu7fmrdzi3y/rlib/R/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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] QuasR_1.17.0          Rbowtie_1.17.0        GenomicRanges_1.29.12
[4] GenomeInfoDb_1.13.4   IRanges_2.11.12       S4Vectors_0.15.6     
[7] BiocGenerics_0.23.0  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               RColorBrewer_1.1-2        
 [3] BiocInstaller_1.27.3       compiler_3.5.0            
 [5] XVector_0.17.1             prettyunits_1.0.2         
 [7] progress_1.1.2             GenomicFeatures_1.29.8    
 [9] bitops_1.0-6               GenomicFiles_1.13.10      
[11] tools_3.5.0                zlibbioc_1.23.0           
[13] biomaRt_2.33.4             digest_0.6.12             
[15] bit_1.1-12                 BSgenome_1.45.1           
[17] RSQLite_2.0                memoise_1.1.0             
[19] tibble_1.3.4               lattice_0.20-35           
[21] rlang_0.1.2                Matrix_1.2-11             
[23] DelayedArray_0.3.19        DBI_0.7                   
[25] GenomeInfoDbData_0.99.1    hwriter_1.3.2             
[27] stringr_1.2.0              rtracklayer_1.37.3        
[29] Biostrings_2.45.4          bit64_0.9-7               
[31] grid_3.5.0                 Biobase_2.37.2            
[33] R6_2.2.2                   AnnotationDbi_1.39.2      
[35] XML_3.98-1.9               BiocParallel_1.11.6       
[37] latticeExtra_0.6-28        magrittr_1.5              
[39] blob_1.1.0                 Rsamtools_1.29.1          
[41] matrixStats_0.52.2         GenomicAlignments_1.13.5  
[43] ShortRead_1.35.1           assertthat_0.2.0          
[45] SummarizedExperiment_1.7.5 stringi_1.1.5             
[47] RCurl_1.95-4.8             VariantAnnotation_1.23.8  
>
omsai commented 7 years ago

Reported to bioconductor mailing list: https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011459.html