Question: Gaia Package Load CNV Error
0
gravatar for Talip Zengin
6 months ago by
Talip Zengin10
Mugla, Turkiye
Talip Zengin10 wrote:

Hi. I use gaia package in a linux server to analyze significant CNVs in TCGA samples. During the process load_cnv command takes very very long time and at the end, it gives an error below.

Loading Copy Number Data
....................................................................................................................................$
Calls: load_cnv
Execution halted

Gaia package gave this error before and I updated the package the newest version but it gives this error again. I try to analyze only 80 samples. If I can manage this , I will analyze ~500 samples.

I could not understand the cause of error. Is it possible that there is a bug in the code? I don't know how to find a bug and fix it.

Thanks in advance.

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /truba/home/tzengin/R/lib64/R/lib/libRblas.so
LAPACK: /truba/home/tzengin/R/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=tr_TR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=tr_TR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=tr_TR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=tr_TR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] gaia_2.26.0         readr_1.3.1         downloader_0.4     
[4] TCGAbiolinks_2.10.4

loaded via a namespace (and not attached):
  [1] backports_1.1.3               circlize_0.4.5               
  [3] AnnotationHub_2.14.4          aroma.light_3.12.0           
  [5] plyr_1.8.4                    selectr_0.4-1                
  [7] ConsensusClusterPlus_1.46.0   lazyeval_0.2.1               
  [9] splines_3.5.2                 BiocParallel_1.16.6          
 [11] GenomeInfoDb_1.18.2           ggplot2_3.1.0                
 [13] sva_3.30.1                    digest_0.6.18                
 [15] foreach_1.4.4                 htmltools_0.3.6              
 [17] magrittr_1.5                  memoise_1.1.0                
 [19] cluster_2.0.7-1               doParallel_1.0.14            
 [21] limma_3.38.3                  ComplexHeatmap_1.20.0        
 [23] Biostrings_2.50.2             annotate_1.60.0              
 [25] matrixStats_0.54.0            sesameData_1.0.0             
 [27] R.utils_2.8.0                 prettyunits_1.0.2            
 [29] colorspace_1.4-0              blob_1.1.1                   
 [31] rvest_0.3.2                   ggrepel_0.8.0                
 [33] xfun_0.5                      dplyr_0.8.0.1                
 [35] crayon_1.3.4                  RCurl_1.95-4.11              
 [37] jsonlite_1.6                  genefilter_1.64.0            
 [39] survival_2.43-3               zoo_1.8-4                    
 [41] iterators_1.0.10              glue_1.3.0                   
 [43] survminer_0.4.3               gtable_0.2.0                 
 [45] sesame_1.0.0                  zlibbioc_1.28.0              
 [47] XVector_0.22.0                GetoptLong_0.1.7             
 [49] DelayedArray_0.8.0            wheatmap_0.1.0               
 [51] shape_1.4.4                   BiocGenerics_0.28.0          
 [53] scales_1.0.0                  DESeq_1.34.1                 
 [55] DBI_1.0.0                     edgeR_3.24.3                 
 [57] ggthemes_4.1.0                Rcpp_1.0.0                   
 [59] xtable_1.8-3                  progress_1.2.0               
 [61] cmprsk_2.2-7                  bit_1.1-14                   
 [63] matlab_1.0.2                  preprocessCore_1.44.0        
 [65] km.ci_0.5-2                   stats4_3.5.2                 
 [67] httr_1.4.0                    RColorBrewer_1.1-2           
 [69] pkgconfig_2.0.2               XML_3.98-1.17                
 [71] R.methodsS3_1.7.1             locfit_1.5-9.1               
 [73] DNAcopy_1.56.0                tidyselect_0.2.5             
 [75] rlang_0.3.1                   later_0.8.0                  
 [77] AnnotationDbi_1.44.0          munsell_0.5.0                
 [79] tools_3.5.2                   generics_0.0.2               
 [81] RSQLite_2.1.1                 ExperimentHub_1.8.0          
 [83] broom_0.5.1                   stringr_1.4.0                
 [85] yaml_2.2.0                    knitr_1.21                   
 [87] bit64_0.9-7                   survMisc_0.5.5               
 [89] purrr_0.3.1                   randomForest_4.6-14          
 [91] EDASeq_2.16.3                 nlme_3.1-137                 
 [93] mime_0.6                      R.oo_1.22.0                  
 [95] xml2_1.2.0                    biomaRt_2.38.0               
 [97] compiler_3.5.2                curl_3.3                     
 [99] interactiveDisplayBase_1.20.0 tibble_2.0.1                 
[101] geneplotter_1.60.0            stringi_1.3.1                
[103] GenomicFeatures_1.34.3        lattice_0.20-38              
[105] Matrix_1.2-15                 KMsurv_0.1-5                 
[107] pillar_1.3.1                  BiocManager_1.30.4           
[109] GlobalOptions_0.1.0           data.table_1.12.0            
[111] bitops_1.0-6                  httpuv_1.4.5.1               
[113] rtracklayer_1.42.2            GenomicRanges_1.34.0         
[115] R6_2.4.0                      latticeExtra_0.6-28          
[117] hwriter_1.3.2                 promises_1.0.1               
[119] ShortRead_1.40.0              gridExtra_2.3                
[121] IRanges_2.16.0                codetools_0.2-16             
[123] assertthat_0.2.0              SummarizedExperiment_1.12.0  
[125] rjson_0.2.20                  GenomicAlignments_1.18.1     
[127] Rsamtools_1.34.1              S4Vectors_0.20.1             
[129] GenomeInfoDbData_1.2.0        mgcv_1.8-27                  
[131] parallel_3.5.2                hms_0.4.2                    
[133] grid_3.5.2                    tidyr_0.8.3                  
[135] ggpubr_0.2                    Biobase_2.42.0               
[137] shiny_1.2.0
gaia load_cnv • 119 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by Talip Zengin10
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