Question: pd.hta.2.0 not installed with Bioconductor 3.5 BiocInstaller 1.26.0 R 3.4.1
0
gravatar for alexander2073
2.1 years ago by
alexander20730 wrote:

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("pd.hta.2.0")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘pd.hta.2.0’
installing the source package ‘pd.hta.2.0’

trying URL 'https://bioconductor.org/packages/3.5/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' ...
** R
** data
** inst
** preparing package for lazy loading
Error: package or namespace load failed for 'oligoClasses' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'iterators'
Error : package 'oligoClasses' could not be loaded
ERROR: lazy loading failed for package 'pd.hta.2.0'
* removing 'C:/Users/xiuch/Documents/R/win-library/3.4/pd.hta.2.0'

The downloaded source packages are in
        ‘C:\Users\xiuch\AppData\Local\Temp\RtmpeMvPaH\downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Warning messages:
1: running command '"C:/PROGRA~1/R/R-3.4.1/bin/x64/R" CMD INSTALL -l "C:\Users\xiuch\Documents\R\win-library\3.4" C:\Users\xiuch\AppData\Local\Temp\RtmpeMvPaH/downloaded_packages/pd.hta.2.0_3.12.2.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘pd.hta.2.0’ had non-zero exit status
>

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by alexander20730

Your answer seems to be here :

Error: package or namespace load failed for 'oligoClasses' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'iterators'
Error : package 'oligoClasses' could not be loaded
ERROR: lazy loading failed for package 'pd.hta.2.0'
* removing 'C:/Users/xiuch/Documents/R/win-library/3.4/pd.hta.2.0'

Have you checked if Oligo and iterators package are correctly installed ?

ADD REPLYlink written 2.1 years ago by giroudpaul40
Answer: pd.hta.2.0 not installed with Bioconductor 3.5 BiocInstaller 1.26.0 R 3.4.1
0
gravatar for alexander2073
2.1 years ago by
alexander20730 wrote:

Thank you giroudpaul for your comments. It works now. It is important to notice that pd.hta.2.0 depends on 

  R (>= 3.2.0), Biostrings(>= 2.35.12), methods, RSQLite (>= 1.0.0), oligoClasses(>= 1.29.6), oligo(>= 1.31.5), DBI (>= 0.3.1), IRanges(>= 2.1.43), S4Vectors(>= 0.5.22).

 

ADD COMMENTlink written 2.1 years ago by alexander20730
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