Issues with trying to download destiny.

[Kensei-K]

I'm trying to download destiny package using BiocManager.

I get the following error message and I'm not sure how to troublshoot it! I appreciate your help!

BiocManager::install("destiny")
---------------------------
Error Message: 
Bioconductor version 3.11 (BiocManager 1.30.10), R
  4.0.2 (2020-06-22)
Installing package(s) 'destiny'
cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES.gz': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES.gz': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES.gz': HTTP status was '404 Not Found'Package which is only available in source form,
  and may need compilation of C/C++/Fortran:
  ‘destiny’

sessionInfo()
---------------------------
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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 
[6] methods   base     

other attached packages:
[1] pheatmap_1.0.12    matrixStats_0.56.0
[3] edgeR_3.30.3       limma_3.44.3      
[5] ggplot2_3.3.2      Seurat_3.1.5      

loaded via a namespace (and not attached):
 [1] nlme_3.1-148        tsne_0.1-3         
 [3] RcppAnnoy_0.0.16    RColorBrewer_1.1-2 
 [5] httr_1.4.1          sctransform_0.2.1  
 [7] tools_4.0.2         R6_2.4.1           
 [9] irlba_2.3.3         KernSmooth_2.23-17 
[11] uwot_0.1.8          lazyeval_0.2.2     
[13] colorspace_1.4-1    withr_2.2.0        
[15] tidyselect_1.1.0    gridExtra_2.3      
[17] curl_4.3            compiler_4.0.2     
[19] plotly_4.9.2.1      labeling_0.3       
[21] scales_1.1.1        lmtest_0.9-37      
[23] ggridges_0.5.2      pbapply_1.4-2      
[25] stringr_1.4.0       digest_0.6.25      
[27] rmarkdown_2.3       pkgconfig_2.0.3    
[29] htmltools_0.5.0     htmlwidgets_1.5.1  
[31] rlang_0.4.7         rstudioapi_0.11    
[33] generics_0.0.2      farver_2.0.3       
[35] zoo_1.8-8           jsonlite_1.7.0     
[37] ica_1.0-2           dplyr_1.0.0        
[39] magrittr_1.5        patchwork_1.0.1    
[41] Matrix_1.2-18       Rcpp_1.0.5         
[43] munsell_0.5.0       ape_5.4            
[45] reticulate_1.16     lifecycle_0.2.0    
[47] stringi_1.4.6       yaml_2.2.1         
[49] MASS_7.3-51.6       Rtsne_0.15         
[51] plyr_1.8.6          grid_4.0.2         
[53] parallel_4.0.2      listenv_0.8.0      
[55] ggrepel_0.8.2       crayon_1.3.4       
[57] lattice_0.20-41     cowplot_1.0.0      
[59] splines_4.0.2       locfit_1.5-9.4     
[61] knitr_1.29          pillar_1.4.6       
[63] igraph_1.2.5        future.apply_1.6.0 
[65] reshape2_1.4.4      codetools_0.2-16   
[67] leiden_0.3.3        glue_1.4.1         
[69] evaluate_0.14       remotes_2.2.0      
[71] data.table_1.12.8   BiocManager_1.30.10
[73] png_0.1-7           vctrs_0.3.1        
[75] gtable_0.3.0        RANN_2.6.1         
[77] purrr_0.3.4         tidyr_1.1.0        
[79] future_1.18.0       xfun_0.15          
[81] rsvd_1.0.3          survival_3.2-3     
[83] viridisLite_0.3.0   tibble_3.0.3       
[85] cluster_2.1.0       globals_0.12.5     
[87] fitdistrplus_1.1-1  ellipsis_0.3.1     
[89] ROCR_1.0-11        

[flying-sheep]

See here: https://stackoverflow.com/questions/43691807/warning-in-install-packages-cannot-open-ur-http-status-was-404-not-found

seems to be a RStudio bug.

[Kensei-K]

The issue was fixed after downloading XCode and gfortran!

So I doubt that it was an issue with RStudio.

It seems to me that my Mac was not able to compile whatever necessary to download destiny!

[flying-sheep]

Yup, problems are always along those lines. The package itself has no problematic parts that could result in any problem when installing it.