Question

DECIPHER version bug using biocLite()

0

Entering edit mode

Vinicius Henrique da Silva ▴ 40

@vinicius-henrique-da-silva-6713

Last seen 19 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 • 1.8k views

ADD COMMENT • link 8.6 years ago Vinicius Henrique da Silva ▴ 40

0

Entering edit mode

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

ADD REPLY • link 8.6 years ago Julian Gehring ★ 1.3k

0

Entering edit mode

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

ADD REPLY • link 8.5 years ago Vinicius Henrique da Silva ▴ 40

Dan Tenenbaum · Answer 1 · 2016-06-09

1

Entering edit mode

Erik Wright ▴ 10

@erik-wright-7838

Last seen 7.2 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

ADD COMMENT • link updated 8.6 years ago by Dan Tenenbaum ★ 8.2k • written 8.6 years ago by Erik Wright ▴ 10

0

Entering edit mode

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.

ADD REPLY • link 8.6 years ago Hervé Pagès 16k

0

Entering edit mode

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

ADD REPLY • link 8.5 years ago Martin Morgan 25k