Entering edit mode
Dear member of this group:
I got strange error when I update bioconductor to latest version 3.2, and I could not install GenomicRanges, IRanges packages. Here is the error what I ran into:
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=Uyghur_China.1256 LC_CTYPE=Uyghur_China.1256 [3] LC_MONETARY=Uyghur_China.1256 LC_NUMERIC=C [5] LC_TIME=Uyghur_China.1256 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.20.1 loaded via a namespace (and not attached): [1] tools_3.2.0
then, I tried to install GenomicRanges packages but can not have it. I got error like this:
install.packages("GenomicRanges")
Installing package into ‘C:/Users/Jvret/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘GenomicRanges’ is not available (for R version 3.2.0)
why this happens ? How can I fix this bug? Please help me out !!
You can see that R is reporting version 3.2.0. The current release version of R is 3.2.3.
The way to install any Bioconductor package is listed on its landing page, e.g., for GenomicRanges
biocLite("GenomicRanges")Dear Martin Morgan:
I have tried this already but did not work. I got same error like this:
biocLite("GenomicRanges") BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.0 (2015-04-16). Installing package(s) ‘GenomicRanges’ also installing the dependencies ‘zlibbioc’, ‘S4Vectors’, ‘IRanges’, ‘XVector’ There is a binary version available but the source version is later: binary source needs_compilation GenomicRanges 1.22.3 1.22.4 TRUE Binaries will be installed trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/zlibbioc_1.16.0.zip' Content type 'application/zip' length 693613 bytes (677 KB) downloaded 677 KB trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/S4Vectors_0.8.11.zip' Content type 'application/zip' length 1755464 bytes (1.7 MB) downloaded 1.7 MB trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/IRanges_2.4.6.zip' Content type 'application/zip' length 3088977 bytes (2.9 MB) downloaded 2.9 MB trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/XVector_0.10.0.zip' Content type 'application/zip' length 749339 bytes (731 KB) downloaded 731 KB trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/GenomicRanges_1.22.3.zip' Content type 'application/zip' length 3028504 bytes (2.9 MB) downloaded 2.9 MB package ‘zlibbioc’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘zlibbioc’ package ‘S4Vectors’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘S4Vectors’ package ‘IRanges’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘IRanges’ package ‘XVector’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘XVector’ package ‘GenomicRanges’ successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package ‘GenomicRanges’ The downloaded binary packages are in C:\Users\Jvret\AppData\Local\Temp\Rtmp0GNchN\downloaded_packages Old packages: 'TxDb.Dmelanogaster.UCSC.dm3.ensGene', 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival' Update all/some/none? [a/s/n]:then, I did like this:
install.packages("GenomicRanges") Installing package into ‘C:/Users/Jvret/Documents/R/win-library/3.2’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘GenomicRanges’ is not available (for R version 3.2.0) > library(GenomicRanges) Error in library(GenomicRanges) : there is no package called ‘GenomicRanges’before, I used old version of biocondutor package and it works perfectly, I could install both GenomicRanges and IRanges packages. Now, I have updated new bioconductor but GenomicRanges package cannot be installed. Thanks a lot !
So instead of the error "there is no package called 'GenomicRanges'", the recommended procedure leads to the warning that R could not "remove prior installation of package 'GenomicRanges'".
This means that one user (maybe 'Administrator') installed GenomicRanges, but another (non-administrator) user tried to update it. Your computer is in a mess, and needs to be cleaned up. There are many ways to do this.
I suggest that as administrator you start R and run the command
.libPaths(). Then quit R, remove the version of R that you have installed, and remove the directories reported by .libPaths().As your regular user, install R version 3.2.3. Start that version of R, and run the command
source("http://bioconductor.org/biocLite.R")Install any other packages, from Bioconductor or CRAN, using biocLite(), e.g,.
biocLite(c("GenomicRanges", "TxDb.Dmelanogaster.UCSC.dm3.ensGene"))Dear Martin Morgan:
Thanks a lot for your help. I have cleared all mass from the past. Now problem solved. Thanks a lot !!