Question: Warning message RSQLite::Id in CummeRbund
gravatar for alexandra.holden.2015
8 weeks ago by
alexandra.holden.20150 wrote:



When trying to use >library(cummeRbund) in R, we keep getting a warning message as the following:

Warning message:
replacing previous import by ‘RSQLite::Id’ when loading ‘AnnotationDbi’

When creating our database we keep getting 0 values for the 'cuff<-readCufflinks()' output - is the warning message when we open the library(cummeRbund) causing this?  How do we fix the warning message?



ADD COMMENTlink modified 8 weeks ago by James W. MacDonald46k • written 8 weeks ago by alexandra.holden.20150
gravatar for James W. MacDonald
8 weeks ago by
United States
James W. MacDonald46k wrote:

 I don't get that message when loading cummeRbund. Are you using a current version of R/Bioconductor?

> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: RSQLite
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':


Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':


Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':


The following object is masked from 'package:IRanges':


The following object is masked from 'package:BiocGenerics':


> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /data/oldR/R-3.5.0/lib64/R/lib/
LAPACK: /data/oldR/R-3.5.0/lib64/R/lib/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] cummeRbund_2.22.0    Gviz_1.24.0          rtracklayer_1.40.1  
 [4] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0  IRanges_2.14.4      
 [7] S4Vectors_0.18.1     fastcluster_1.1.24   reshape2_1.4.3      
[10] ggplot2_2.2.1        RSQLite_2.1.1        BiocGenerics_0.26.0
[13] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] Biobase_2.40.0              httr_1.3.1                 
 [3] bit64_0.9-7                 splines_3.5.0              
 [5] Formula_1.2-3               assertthat_0.2.0           
 [7] latticeExtra_0.6-28         blob_1.1.1                 
 [9] BSgenome_1.48.0             GenomeInfoDbData_1.1.0     
[11] Rsamtools_1.32.0            progress_1.1.2             
[13] pillar_1.2.2                backports_1.1.2            
[15] lattice_0.20-35             biovizBase_1.28.0          
[17] digest_0.6.15               RColorBrewer_1.1-2         
[19] XVector_0.20.0              checkmate_1.8.5            
[21] colorspace_1.3-2            htmltools_0.3.6            
[23] Matrix_1.2-14               plyr_1.8.4                 
[25] XML_3.98-1.11               GetoptLong_0.1.6           
[27] biomaRt_2.36.0              zlibbioc_1.26.0            
[29] scales_0.5.0                BiocParallel_1.14.1        
[31] tibble_1.4.2                htmlTable_1.11.2           
[33] AnnotationFilter_1.4.0      GenomicFeatures_1.32.0     
[35] SummarizedExperiment_1.10.0 nnet_7.3-12                
[37] lazyeval_0.2.1              survival_2.42-3            
[39] magrittr_1.5                memoise_1.1.0              
[41] foreign_0.8-70              data.table_1.11.0          
[43] tools_3.5.0                 prettyunits_1.0.2          
[45] GlobalOptions_0.0.13        matrixStats_0.53.1         
[47] ComplexHeatmap_1.18.0       stringr_1.3.0              
[49] munsell_0.4.3               cluster_2.0.7-1            
[51] DelayedArray_0.6.0          ensembldb_2.4.1            
[53] AnnotationDbi_1.42.0        Biostrings_2.48.0          
ADD COMMENTlink written 8 weeks ago by James W. MacDonald46k
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