I am starting Bioconductor by following Kasper Hansens lectures. Now I cannot get the GenomicRanges library to load. I can see the package in my package tab in R studio so it seems to be there but it will not run. I loaded biocLite() freshly to start . There seems to be a problem with GenomeInfoDb() but what is it?
Thanks a lot for any help.
Here is the output;
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Old packages: 'GenomicRanges', 'IRanges', 'manipulate', 'S4Vectors'
Update all/some/none? [a/s/n]:
a
Warning: packages ‘IRanges’, ‘S4Vectors’ are in use and will not be installed
trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/GenomicRanges_1.28.5.zip'
Content type 'application/zip' length 3005132 bytes (2.9 MB)
downloaded 2.9 MB
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.4/manipulate_1.0.1.zip'
Content type 'application/zip' length 35982 bytes (35 KB)
downloaded 35 KB
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘manipulate’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\William Brown\AppData\Local\Temp\RtmpEvBBDz\downloaded_packages
> biocLite(GenomicRanges)
Error in "BiocUpgrade" %in% pkgs : object 'GenomicRanges' not found
> library("GenomicRanges", lib.loc="~/R/win-library/3.4")
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded
> biocLite(GenomicRanges)
Error in "BiocUpgrade" %in% pkgs : object 'GenomicRanges' not found
> library("GenomeInfoDb", lib.loc="~/R/win-library/3.4")
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
and
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.26.1 IRanges_2.10.2 S4Vectors_0.14.3 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1 RCurl_1.95-4.8 bitops_1.0-6
Thanks That was helpful I just needed to use biocLite("GenomeInfoDbData"). It was the inverted commas that were missing.
I was wrong; it seemed to have loaded but when I came to load GRnages() it could not be seen.
> biocLite("GenomeInfoDbData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘GenomeInfoDbData’
installing the source package ‘GenomeInfoDbData’
trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz'
Content type 'application/x-gzip' length 16238792 bytes (15.5 MB)
downloaded 15.5 MB
Error: '\P' is an unrecognized escape in character string starting ""C:\P"
Execution halted
The downloaded source packages are in
‘C:\Users\William Brown\AppData\Local\Temp\RtmpS8HQDc\downloaded_packages’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Old packages: 'IRanges', 'manipulate', 'S4Vectors'
Update all/some/none? [a/s/n]:
a
Warning: packages ‘IRanges’, ‘S4Vectors’ are in use and will not be installed
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.4/manipulate_1.0.1.zip'
Content type 'application/zip' length 35982 bytes (35 KB)
downloaded 35 KB
package ‘manipulate’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\William Brown\AppData\Local\Temp\RtmpS8HQDc\downloaded_packages
Warning messages:
1: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\William Brown\Documents\R\win-library\3.4" C:\Users\WILLIA~1\AppData\Local\Temp\RtmpS8HQDc/downloaded_packages/GenomeInfoDbData_0.99.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GenomeInfoDbData’ had non-zero exit status
> library("GenomeInfoDb", lib.loc="~/R/win-library/3.4")
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’