Multiple errors and unavailable packages when trying to install TCGAWorkflow

[leowill01]

I'm doing a fresh install of R/RStudio. When I go to install TCGAWorkflow, I get several errors. Here is a summary of all the error lines when running BiocManager::install("TCGAWorkflow"):

1. Warning: dependency ‘MotIV’ is not available
2. download from 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz' failed
3. downloaded length 687399349 != reported length 710245413
4. URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz': Timeout of 60 seconds was reached
5. download of package ‘BSgenome.Hsapiens.UCSC.hg19’ failed
6. there is no package called ‘GenomeInfoDbData’
7. ERROR: lazy loading failed for package ‘TCGAWorkflowData’ 
8. ERROR: dependencies ‘BSgenome.Hsapiens.UCSC.hg19’, ‘MotIV’, ‘TCGAWorkflowData’ are not available for package ‘TCGAWorkflow’
9. installation of package ‘TCGAWorkflowData’ had non-zero exit status
10. installation of package ‘TCGAWorkflow’ had non-zero exit status 

And here is the full console output when trying to install TCGAWorkflow (with error lines marked with "**********"):

> BiocManager::install("TCGAWorkflow")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'TCGAWorkflow'
Warning: dependency ‘MotIV’ is not available ********************
also installing the dependencies ‘BSgenome.Hsapiens.UCSC.hg19’, ‘TCGAWorkflowData’

installing the source packages ‘BSgenome.Hsapiens.UCSC.hg19’, ‘TCGAWorkflowData’, ‘TCGAWorkflow’

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz'
Content type 'application/x-gzip' length 710245413 bytes (677.3 MB)
================================================
downloaded 655.6 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz' failed ********************
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 687399349 != reported length 710245413 ********************
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz': Timeout of 60 seconds was reached ********************
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘BSgenome.Hsapiens.UCSC.hg19’ failed ********************
trying URL 'https://bioconductor.org/packages/3.12/data/experiment/src/contrib/TCGAWorkflowData_1.14.0.tar.gz'
Content type 'application/x-gzip' length 81290283 bytes (77.5 MB)
==================================================
downloaded 77.5 MB

trying URL 'https://bioconductor.org/packages/3.12/workflows/src/contrib/TCGAWorkflow_1.13.0.tar.gz'
Content type 'application/x-gzip' length 5282161 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

* installing *source* package ‘TCGAWorkflowData’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’ ********************
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘TCGAWorkflowData’ ********************
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/TCGAWorkflowData’
ERROR: dependencies ‘BSgenome.Hsapiens.UCSC.hg19’, ‘MotIV’, ‘TCGAWorkflowData’ are not available for package ‘TCGAWorkflow’ ********************
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/TCGAWorkflow’

The downloaded source packages are in
	‘/private/var/folders/gn/0t2vgsl9305g1gm65mh6fbq40000gn/T/Rtmp3rtSe0/downloaded_packages’
Old packages: 'codetools', 'KernSmooth', 'nlme'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
          binary source needs_compilation
codetools 0.2-16 0.2-18             FALSE

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/KernSmooth_2.23-18.tgz'
Content type 'application/x-gzip' length 100133 bytes (97 KB)
==================================================
downloaded 97 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/nlme_3.1-150.tgz'
Content type 'application/x-gzip' length 2379858 bytes (2.3 MB)
==================================================
downloaded 2.3 MB


The downloaded binary packages are in
	/var/folders/gn/0t2vgsl9305g1gm65mh6fbq40000gn/T//Rtmp3rtSe0/downloaded_packages
installing the source package ‘codetools’

trying URL 'https://cran.rstudio.com/src/contrib/codetools_0.2-18.tar.gz'
Content type 'application/x-gzip' length 38175 bytes (37 KB)
==================================================
downloaded 37 KB

* installing *source* package ‘codetools’ ...
** package ‘codetools’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (codetools)

The downloaded source packages are in
	‘/private/var/folders/gn/0t2vgsl9305g1gm65mh6fbq40000gn/T/Rtmp3rtSe0/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘TCGAWorkflowData’ had non-zero exit status ********************
2: In install.packages(...) :
  installation of package ‘TCGAWorkflow’ had non-zero exit status ********************
> 

I'm not sure where to start. I previously had TCGAWorkflow "installed" and was working through some of the vignettes, but it's likely I just didn't notice all these errors when I had installed it previously.

Here's my sessionInfo() for reference:

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

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

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     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3        

Any help would be appreciated, thanks.

[rbtoscan]

Have you found the solution yet?

[leowill01]

@rbtoscan no i gave up and havent felt the need to try again

[tiagochst]

Did you try installing GenomeInfoDbData package ? BiocManager::install("GenomeInfoDbData") Also Bioconductor 3.12 is from 3 years ago. I would update to the latest version 3.17.