[Bioc-devel] Monocle version from biocLite is not the newest version

[Martin Morgan]

On 06/07/2017 11:03 PM, Xiaojie Qiu wrote:
> Dear Bioconductor maintainers,
> 
> We recently received installation issue reports regarding our Monocle
> package from bioconductor. When they use the following code to install the
> package,
> 
> source("https://bioconductor.org/biocLite.R")
> biocLite("monocle")
> 
> They only install the 2.2 version instead of the newest 2.4 version. We

For me I have

 > source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
 > biocLite("monocle")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 Patched (2017-05-24
   r72729).
Installing package(s) ‘monocle’
trying URL 
'https://bioconductor.org/packages/3.5/bioc/src/contrib/monocle_2.4.0.tar.gz'
Content type 'application/x-gzip' length 2073297 bytes (2.0 MB)
...


maybe the problem is that they are using an older version of R and / or 
Bioconductor? To get monocle 2.4.0 requires R-3.4.0 and Bioconductor 
3.5; see http://bioconductor.org/install

 > sessionInfo()
R version 3.4.0 Patched (2017-05-24 r72729)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /home/mtmorgan/bin/R-3-4-branch/lib/libRblas.so
LAPACK: /home/mtmorgan/bin/R-3-4-branch/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.26.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0


Martin


> noticed that there is a building error for our software package which
> appears after bioconductor upgraded to R 3.4 (we will fix that tomorrow or
> so). This may be related to the above issue but the version mismatch should
> not happen. Could you please help us to fix the link to the correct version
> please?
> 
> Much appreciated!
> 
> Xiaojie
> 
> 	[[alternative HTML version deleted]]
> 
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