[Bioc-devel] can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Martin Morgan]

On 11/11/2016 09:44 AM, Jurat Shayidin wrote:
> Dear BiocDevel:
>
> I ran into the issue after installed devel version of R and Bioc 3.4.
> Because my packages depends on some packages from CRAN repository, now I
> failed to installed paclages from CRAN. I don't have problem when I used
> released version of R. Because new packages must coordinate with devel
> version of Bioc and R, so I did it. But can't installl packages from CRAN
> like dplyr. How can I overcome this issue ? Any quick solution ?  I got
> error as follow:
>
>
>> BiocInstaller::useDevel()
> Error: 'devel' version already in use
>> install.packages("dplyr")
> Error in install.packages : missing value where TRUE/FALSE needed

this does not happen for me; you'll need to debug on your end, 
minimally, reporting the output of traceback() after the error occurs.

are you in a clean R session with no .RData or other objects loaded that 
might interfere with R?

   R --vanilla

Martin

PS -- please do not 'close' questions that have been answered on 
support.bioconductor.org.

>>
>
>> sessionInfo()
> R Under development (unstable) (2016-11-09 r71642)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows >= 8 x64 (build 9200)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices
> [6] utils     datasets  methods   base
>
> other attached packages:
>  [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
>  [3] XVector_0.15.0             rtracklayer_1.35.1
>  [5] GenomicRanges_1.27.5       GenomeInfoDb_1.11.3
>  [7] IRanges_2.9.7              S4Vectors_0.13.2
>  [9] BiocGenerics_0.21.0        BiocInstaller_1.25.2
>
> loaded via a namespace (and not attached):
>  [1] lattice_0.20-34          XML_3.98-1.5
>  [3] Rsamtools_1.27.2         Biostrings_2.43.0
>  [5] GenomicAlignments_1.11.0 bitops_1.0-6
>  [7] grid_3.4.0               zlibbioc_1.21.0
>  [9] Matrix_1.2-7.1           BiocParallel_1.9.1
> [11] tools_3.4.0              RCurl_1.95-4.8
> [13] compiler_3.4.0
>>
>
>
>


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