Error: object ‘GDCquery_Maf’ is not exported by 'namespace:TCGAbiolinks'

[ymahmoud]

Hi! Thanks for this package. I'm trying to install the package but I get the following error:

> devtools::install_github("ashishjain1988/MAFDash")
Downloading GitHub repo ashishjain1988/MAFDash@HEAD
Skipping 6 packages not available: BSgenome.Hsapiens.UCSC.hg38, IRanges, GenomicRanges, ComplexHeatmap, maftools, TCGAbiolinks
✔  checking for file ‘/private/var/folders/mr/rywc03vj2h3bjg39kpv0mbg80000gn/T/RtmpZAnApd/remotesa8f5425ebbb0/ashishjain1988-MAFDash-3f4a662/DESCRIPTION’ (1.4s)
─  preparing ‘MAFDash’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘MAFDash_0.2.2.tar.gz’

* installing *source* package ‘MAFDash’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘GDCquery_Maf’ is not exported by 'namespace:TCGAbiolinks'
Execution halted
ERROR: lazy loading failed for package ‘MAFDash’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/MAFDash’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/mr/rywc03vj2h3bjg39kpv0mbg80000gn/T//RtmpZAnApd/filea8f5597441da/MAFDash_0.2.2.tar.gz’ had non-zero exit status

Session info:

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.0

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] maftools_2.12.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9          BiocManager_1.30.19 urlchecker_1.0.1    compiler_4.2.1      RColorBrewer_1.1-3  later_1.3.0         remotes_2.4.2      
 [8] profvis_0.3.7       prettyunits_1.1.1   tools_4.2.1         digest_0.6.30       pkgbuild_1.3.1      pkgload_1.3.0       memoise_2.0.1      
[15] lifecycle_1.0.3     lattice_0.20-45     pkgconfig_2.0.3     rlang_1.0.6         Matrix_1.5-1        shiny_1.7.3         cli_3.4.1          
[22] rstudioapi_0.14     curl_4.3.3          fastmap_1.1.0       withr_2.5.0         stringr_1.4.1       htmlwidgets_1.5.4   fs_1.5.2           
[29] vctrs_0.5.0         devtools_2.4.5      rsthemes_0.4.0      hms_1.1.2           rprojroot_2.0.3     grid_4.2.1          glue_1.6.2         
[36] data.table_1.14.4   R6_2.5.1            processx_3.7.0      DNAcopy_1.70.0      survival_3.4-0      sessioninfo_1.2.2   purrr_0.3.5        
[43] callr_3.7.2         magrittr_2.0.3      usethis_2.1.6       promises_1.2.0.1    ps_1.7.1            ellipsis_0.3.2      htmltools_0.5.3    
[50] splines_4.2.1       mime_0.12           xtable_1.8-4        httpuv_1.6.6        stringi_1.7.8       miniUI_0.1.1.1      cachem_1.0.6       
[57] crayon_1.5.2

I think this is related to the GDCquery_Maf function that was removed from the latest versions of TCGAbiolinks.

[Rohit-Satyam]

I am facing the same issue. When will this issue be resolved?

[ashishjain1988]

@ymahmoud Sorry for the late reply. This error is coming due to the changes in the latest of the TCGABiolinks package. I will try to comment of the code that is using TCGAbiolinks.

@Rohit-Satyam

[ashishjain1988]

I commented out the code that were using TCGAbiolinks functions. Please try to install the package with the latest code. I will create a new issue to update the function to get TCGA datasets.