Problem with pd.hta.2.0 package installation
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Entering edit mode
@user-24975
Last seen 5 weeks ago

Have been trying to download package pd.hta.2.0 with no success. I have tried on multiple computers, different R versions (4.0.3 & 4.0.4 respectively), different internet sources, etc. I continually get a timeout message. I haven't on my way found any good alternatives for downloading the package (I'm not an expert in this area and don't want to mess up my libraries or something by accident).

Context: I need it to run an analysis on some microarray data from Thermofisher/affymetrix using oligo. Oligo will not run without the correct annotation package, which in my case is pd.hta.2.0

BiocManager::install("pd.hta.2.0")

Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'pd.hta.2.0'
installing the source package ‘pd.hta.2.0’

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz'
Content type 'application/x-gzip' length 373269686 bytes (356.0 MB)
====
downloaded 31.7 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 33235440 != reported length 373269686
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘pd.hta.2.0’ failed

sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

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  methods   base     

other attached packages:
[1] XML_3.99-0.5

loaded via a namespace (and not attached):
 [1] crayon_1.4.1        dplyr_1.0.5         R6_2.5.0            lifecycle_1.0.0     magrittr_2.0.1     
 [6] pillar_1.5.1        rlang_0.4.10        vctrs_0.3.6         generics_0.1.0      ellipsis_0.3.1     
[11] tools_4.0.3         glue_1.4.2          purrr_0.3.4         yaml_2.2.1          compiler_4.0.3     
[16] pkgconfig_2.0.3     BiocManager_1.30.10 tidyselect_1.1.0    tibble_3.1.0
Install • 63 views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 8 hours ago
United States

I'd try again. It's probably just an intermittent issue, as I can install without problems:

> install("pd.hta.2.0")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'pd.hta.2.0'
installing the source package 'pd.hta.2.0'

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz'
Content type 'application/x-gzip' length 373269686 bytes (356.0 MB)
downloaded 356.0 MB

* installing *source* package 'pd.hta.2.0' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pd.hta.2.0'
    finding HTML links ... done
    pkg                                     html  
    probeSequences                          html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (pd.hta.2.0)

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