Error faced for library(TCGAbiolinks)

Question

[gokce.ouz]

Hi,

I am working on server. Whenever I want to use library(TCGAbiolinks) I am facing the error below. How could I solve this problem ?

Thanks in advance,

Gokce

Error: package or namespace load failed for âTCGAbiolinksâ: object ârbind.gtableâ is not exported by 'namespace:gridExtra'

sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

Matrix products: default
BLAS: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRblas.so
LAPACK: /mnt/software/stow/R-3.4.1/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_0.7.3          BiocInstaller_1.26.1

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            selectr_0.3-1              
  [3] rjson_0.2.15                hwriter_1.3.2              
  [5] class_7.3-14                modeltools_0.2-21          
  [7] mclust_5.3                  circlize_0.4.1             
  [9] XVector_0.16.0              GenomicRanges_1.28.5       
 [11] GlobalOptions_0.0.12        ggrepel_0.6.5              
 [13] flexmix_2.3-14              bit64_0.9-7                
 [15] AnnotationDbi_1.38.2        mvtnorm_1.0-6              
 [17] xml2_1.1.1                  codetools_0.2-15           
 [19] splines_3.4.1               R.methodsS3_1.7.1          
 [21] doParallel_1.0.10           DESeq_1.28.0               
 [23] robustbase_0.92-7           geneplotter_1.54.0         
 [25] Rsamtools_1.28.0            annotate_1.54.0            
 [27] cluster_2.0.6               kernlab_0.9-25             
 [29] R.oo_1.21.0                 readr_1.1.1                
 [31] compiler_3.4.1              httr_1.3.1                 
 [33] assertthat_0.2.0            Matrix_1.2-11              
 [35] lazyeval_0.2.0              limma_3.32.6               
 [37] tools_3.4.1                 bindrcpp_0.2               
 [39] gtable_0.2.0                glue_1.1.1                 
 [41] GenomeInfoDbData_0.99.0     ggthemes_3.4.0             
 [43] ShortRead_1.34.1            Rcpp_0.12.12               
 [45] Biobase_2.36.2              trimcluster_0.1-2          
 [47] Biostrings_2.44.2           rtracklayer_1.36.4         
 [49] iterators_1.0.8             fpc_2.1-10                 
 [51] stringr_1.2.0               XML_3.98-1.9               
 [53] dendextend_1.5.2            edgeR_3.18.1               
 [55] DEoptimR_1.0-8              zlibbioc_1.22.0            
 [57] MASS_7.3-47                 scales_0.5.0               
 [59] aroma.light_3.6.0           hms_0.3                    
 [61] parallel_3.4.1              SummarizedExperiment_1.6.3 
 [63] RColorBrewer_1.1-2          ComplexHeatmap_1.14.0      
 [65] memoise_1.1.0               gridExtra_2.3              
 [67] ggplot2_2.2.1               downloader_0.4             
 [69] biomaRt_2.32.1              latticeExtra_0.6-28        
 [71] stringi_1.1.5               RSQLite_2.0                
 [73] genefilter_1.58.1           S4Vectors_0.14.4           
 [75] foreach_1.4.3               GenomicFeatures_1.28.4     
 [77] BiocGenerics_0.22.0         BiocParallel_1.10.1        
 [79] shape_1.4.3                 GenomeInfoDb_1.12.2        
 [81] rlang_0.1.2                 pkgconfig_2.0.1            
 [83] prabclus_2.2-6              matrixStats_0.52.2         
 [85] bitops_1.0-6                lattice_0.20-35            
 [87] bindr_0.1                   GenomicAlignments_1.12.2   
 [89] bit_1.1-12                  plyr_1.8.4                 
 [91] magrittr_1.5                R6_2.2.2                   
 [93] IRanges_2.10.3              DelayedArray_0.2.7         
 [95] DBI_0.7                     whisker_0.3-2              
 [97] survival_2.41-3             RCurl_1.95-4.8             
 [99] nnet_7.3-12                 tibble_1.3.4               
[101] EDASeq_2.10.0               viridis_0.4.0              
[103] GetoptLong_0.1.6            locfit_1.5-9.1             
[105] grid_3.4.1                  data.table_1.10.4          
[107] blob_1.1.0                  ConsensusClusterPlus_1.40.0
[109] digest_0.6.12               diptest_0.75-7             
[111] xtable_1.8-2                R.utils_2.5.0              
[113] stats4_3.4.1                munsell_0.4.3              
[115] viridisLite_0.2.0

Answer 1

[russhh]

From the NEWS for gridExtra 2.3: https://cran.r-project.org/web/packages/gridExtra/news.html

Misc. cleanup for CRAN release

renamed cbind/rbind functions copied from gtable to cbind_gtable and rbind_gtable to avoid issues with generic method (different signature) more consistency in gtable-related functions

This suggests that the version of tcgabiolinks that you've installed is unaware that rbind.gtable has been renamed rbind_gtable within gridExtra. Remove your install of gridExtra using remove.packages and install version 2.2

And post an issue to the tcgabiolinks on github

[gokce.ouz]

Thanks for your reply and clarification. I raised an issue as you suggested.