DECIPHER version bug using biocLite()
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@vinicius-henrique-da-silva-6713
Last seen 15 months ago
Brazil

I was trying to use the DECIPHER package today and it was not supporting even the examples in the manual. When I checked, I was using an old version (v 1.16.1). It was strange because I just installed it with:

source("https://bioconductor.org/biocLite.R")
biocLite("DECIPHER")

Thus, I installed manually the more recent version available:

install.packages("~/DECIPHER_2.0.2.tar.gz", repos = NULL, type="source")

And now it seems to be ok with the manual. Why the biocLite function is installing this old version?

Updated to Erik Wright and Julian Gehring. I am using the R 3.3.0 as showed below: 

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] BiocInstaller_1.20.3 DECIPHER_2.0.2       RSQLite_1.0.0
[4] DBI_0.4-1            Biostrings_2.38.4    XVector_0.10.0
[7] IRanges_2.4.8        S4Vectors_0.8.11     BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 tools_3.3.0

And below you can see the behavior of the biocLite() function with the above 'version setting' (already with the last DECIPHER version): 

> biocLite("DECIPHER")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.0 (2016-05-03).
Installing package(s) ‘DECIPHER’
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/DECIPHER_1.16.1.tar.gz'
Content type 'unknown' length 7621858 bytes (7.3 MB)
==================================================
downloaded 7.3 MB

There is just one more recent R version, which is not even launched. I am missing something?

 

 

DECIPHER • 780 views
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What version of R / Bioconductor are you using? You can find this out from the output of sessionInfo() and biocVersion()?

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Hi Julian. Please check my update. I was unable to identify what was wrong with my versions. 

1
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Erik Wright ▴ 10
@erik-wright-7838
Last seen 3.8 years ago
United States
Hi Vinicius, The biocLite() function will match the installed packages to the version of R that you are using. If you are using the last version of R (3.2) then it will install the corresponding version of DECIPHER (v1.16.1). You should upgrade your R to the latest release in order to use the most recent version of DECIPHER. I hope that helps! Erik
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Hi Erik,

Note that the last version of R is 3.3. This is the version needed in order to run the current release of Bioconductor which is also 3.3. In BioC 3.3, DECIPHER is currently at version 2.0.2.

Cheers,

H.

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BiocInstaller is at version 1.20.0 in your system, but the version for R 3.3.0 is 1.22.2. Follow these directions for updating BiocInstaller. There should be a message when BiocInstaller is installed that

> library(BiocInstaller)
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
Warning message:
BiocInstaller version 3.2 is too old for R version 3.3.0; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller 

 

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