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rwdavies / STITCH

STITCH - Sequencing To Imputation Through Constructing Haplotypes
http://www.nature.com/ng/journal/v48/n8/abs/ng.3594.html
GNU General Public License v3.0
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error #9

Closed smangul1 closed 5 years ago

smangul1 commented 6 years ago

Hi,

I have got this error when running : ./scripts/install-dependencies.sh

R preparing package for lazy loading ** help * installing help indices building package indices ** testing if installed package can be loaded

is it a problem?

Thanks, Serghei

smangul1 commented 6 years ago

Also another error

configure: error: liblzma not found, please install lzma (http://www.7-zip.org/sdk.html) make: *** [SeqLib] Error 1 ERROR: compilation failed for package ‘STITCH’

rwdavies commented 6 years ago

Hm, the warning message is weird, but I just checked and it shows up in the build (https://travis-ci.org/rwdavies/STITCH/jobs/410058195#L2547) which is passing. If you open R is the library installed? (i.e. type "R" on command line then library("rrbgen") )

The lzma one is more annoying. This comes from the SeqLib dependency which I've seen before e.g. https://github.com/walaj/bxtools/issues/19 and the related https://github.com/samtools/htslib/issues/490 Are you able to ask an admin to install? Otherwise I've installed it myself without admin rights but it's annoying. I'll see if I can dig up the script and generalize it into stitch if lzma is not found

rwdavies commented 6 years ago

Hey, for the lzma / xz thing, I added a script and some instructions for how to install xz locally and make available to SeqLib. Can you try running the following and let me know if it works? 

./scripts/install-xz.sh
echo "CPPFLAGS += -I`pwd`/install/include" >> ~/.R/Makevars
echo "LDFLAGS += -I`pwd`/install/lib" >> ~/.R/Makevars
./scripts/build-and-install.sh
rwdavies commented 6 years ago

Sorry I forgot some stuff in the install-xz script. Let me check some things and get back to you

rwdavies commented 6 years ago

Sorry upon further inspection it did work properly on a system I have without xz or gmp etc installed. Let me know if it works for you

rwdavies commented 5 years ago

Closing this as suggestions above should fix this, and otherwise STITCH is in bioconda now and that should prevent this sort of problem