Warning message RSQLite::Id in CummeRbund
1
0
Entering edit mode
@alexandraholden2015-15832
Last seen 4.4 years ago

Hi,

 

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?

 

Thanks!

bioconductor rnaseq cummerbund • 695 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 13 hours ago
United States

 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, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, 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: RSQLite
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

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

    hclust

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':

    expand.grid

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':

    promoters

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

    promoters

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

    conditions


> 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/libRblas.so
LAPACK: /data/oldR/R-3.5.0/lib64/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] 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          
<snip>
ADD COMMENT

Login before adding your answer.

Traffic: 491 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6