Question: Trouble Installing lifOver workflow
0
gravatar for JustGettinStarted
3.0 years ago by
JustGettinStarted0 wrote:

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
ADD COMMENTlink modified 3.0 years ago by James W. MacDonald51k • written 3.0 years ago by JustGettinStarted0

Not an answer to your question but perhaps a solution to your problem: you can also use LiftOver online

ADD REPLYlink written 3.0 years ago by WouterDeCoster110

Thanks WouterDeCoster, i have been doing that, but its not ideal.

ADD REPLYlink written 3.0 years ago by JustGettinStarted0

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

ADD REPLYlink written 3.0 years ago by Valerie Obenchain6.7k

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/xcrun

which 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’
ADD REPLYlink written 3.0 years ago by JustGettinStarted0

Install the binary rather than source version install.packages("stringi", type="binary"). Probably for most users binary installation is appropriate.

ADD REPLYlink written 3.0 years ago by Martin Morgan ♦♦ 23k

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. 

ADD REPLYlink written 3.0 years ago by JustGettinStarted0
Answer: Trouble Installing lifOver workflow
2
gravatar for James W. MacDonald
3.0 years ago by
United States
James W. MacDonald51k wrote:

The liftOver function is part of rtracklayer, so unless you want to work through the workflow, you don't need to install the workflow, just the rtracklayer package. And then if your SNPs are encapsulated in a GRanges, you just import the correct chain file and use liftOver to convert to the correct genome build. As an example, let's liftOver a GRanges from hg19 to hg38:

> download.file("http://hgdownload.cse.ucsc.edu/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz", "hg19ToHg38.over.chain.gz")
trying URL 'http://hgdownload.cse.ucsc.edu/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz'
Content type 'application/x-gzip' length 227698 bytes (222 KB)
==================================================
downloaded 222 KB

> system("gzip -d hg19ToHg38.over.chain.gz")
> chain <- import.chain("hg19ToHg38.over.chain")
> z <- liftOver(rowRanges(finalData), chain)

> class(rowRanges(finalData))
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"
> class(z)
[1] "GRangesList"
attr(,"package")
[1] "GenomicRanges"
ADD COMMENTlink written 3.0 years ago by James W. MacDonald51k

Works great, thanks

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by JustGettinStarted0
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