Entering edit mode
@justgettinstarted-11604
Last seen 8.2 years ago
Hi,
I need to convert several hundred SNPs from one build to another. Went to install the liftOver workflow and the install fails.
I followed the copied the instructions for installing the workflow found here
Specifically;
source("https://bioconductor.org/biocLite.R")
biocLite()
I had no problems here but next part didnt work
source("http://bioconductor.org/workflows.R")
workflowInstall("liftOver")
Warning in install.packages :
URL 'http://bioconductor.org/packages/3.3/workflows/bin/macosx/mavericks/contrib/3.3/PACKAGES.gz': status was '404 Not Found'
Warning in install.packages :
URL 'http://bioconductor.org/packages/3.3/workflows/bin/macosx/mavericks/contrib/3.3/PACKAGES': status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://bioconductor.org/packages/3.3/workflows/bin/macosx/mavericks/contrib/3.3:
cannot download all files
installing the source package ‘liftOver’
trying URL 'http://bioconductor.org/packages/3.3/workflows/src/contrib/liftOver_0.99.120929.tar.gz'
Content type 'application/x-gzip' length 2756637 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
* installing *source* package ‘liftOver’ ...
** inst
** help
No man pages found in package ‘liftOver’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘stringi’
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/liftOver’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/liftOver’
Warning in install.packages :
installation of package ‘liftOver’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/fc/lcgdm6b56zzfrpjjj483ckq40000gn/T/RtmpsAXW9i/downloaded_packages’
I am running R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Any help would be greatly appreciated.
sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.22.3 loaded via a namespace (and not attached): [1] tools_3.3.1
Not an answer to your question but perhaps a solution to your problem: you can also use LiftOver online
Thanks WouterDeCoster, i have been doing that, but its not ideal.
Jim is right and you can use rtracklayer directly. I'd still like to sort out why you can't install the workflow. I've confirmed that the mac binaries and other files are available at the expected location and I am able to install the workflow. The error message says you don't have the stringi package installed:
** testing if installed package can be loaded
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘stringi’
Did you try installing it? If not, please try installing stringi and let me know if it works.
Valerie
Can't seem to be able to install 'stringi'. Get a really lengthly error message but here is the cropped jist of it.
> install.packages("stringi") There is a binary version available but the source version is later: binary source needs_compilation stringi 1.1.1 1.1.2 FALSE installing the source package ‘stringi’ trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.1.2.tar.gz' Content type 'application/x-gzip' length 3644855 bytes (3.5 MB) ================================================== downloaded 3.5 MB * installing *source* package ‘stringi’ ... ** package ‘stringi’ successfully unpacked and MD5 sums checked checking for local ICUDT_DIR... icu55/data checking for R_HOME... /Library/Frameworks/R.framework/Resources checking for R... /Library/Frameworks/R.framework/Resources/bin/R checking for R >= 3.1.0... yes checking for cat... /bin/cat xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrunwhich goes on for a while before ending with
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun checking for gcc... gcc checking whether the C compiler works... no configure: error: in `/private/var/folders/fc/lcgdm6b56zzfrpjjj483ckq40000gn/T/RtmpNhQwhw/R.INSTALL127f1e034d73/stringi': configure: error: C compiler cannot create executables See `config.log' for more details ERROR: configuration failed for package ‘stringi’ * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/stringi’ Warning in install.packages : installation of package ‘stringi’ had non-zero exit status The downloaded source packages are in ‘/private/var/folders/fc/lcgdm6b56zzfrpjjj483ckq40000gn/T/RtmpMoxmHd/downloaded_packages’Install the binary rather than source version
install.packages("stringi", type="binary"). Probably for most users binary installation is appropriate.Boom done! That worked fine and after installing the binary version of 'stringi' i was able to load the workflow. Thanks for your help Martin and Valerie.