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kubovcij
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@kubovcij-19664
Last seen 5.0 years ago
Hello everyone, i have troubles installing Rsamtools on R 3.6.0 (Bioc 3.9) on ubuntu via both BiocManager::install() and source package (v1.99.6). No problem with Rsamtools in previous R version, local instalation of Rsamtools from source package v1.34.1 also worked fine in R 3.6.0. Already tried this old post and changed RHOME/etc/Makeconf flags, but didn't help. Other packages install just fine. Any hint?
> BiocManager::install('Rsamtools')
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'Rsamtools'
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rsamtools_1.99.6.tar.gz'
Content type 'application/x-gzip' length 3032600 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
* installing *source* package ‘Rsamtools’ ...
...compilation...
installing to /home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so':
/home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: faidx_fetch_seq2
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/Rsamtools’
* restoring previous ‘/home/kubovcij/R/x86_64-pc-linux-gnu-library/3.6/Rsamtools’
The downloaded source packages are in
‘/tmp/Rtmpazaaxg/downloaded_packages’
...
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=cs_CZ.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=cs_CZ.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.6.0 tools_3.6.0
Do you have the correct version of Rhtslib? I think that's where
faidx_fetch_seq2is defined. (Based on this commit, you might need version >= 1.13.2). Rsamtools 1.34 didn't require that package, but 1.99.6 does, so if you're upgrading this may be the source of the error.Might be worth doing
BiocManager::install('Rhtslib')and then retrying Rsamtools.thanks for reply, my Rhtslib is 1.15.6. I have run
BiocManager::install('Rhtslib')just to be sure but with no success, got same error when reinstalling Rsamtools. I checked https://bioconductor.org/help/faq/ where same error example is explained as system configuration issue, but i don't know where to check since all was fine in previous version of R.Can you show more of the compilation, of both Rhtslib and Rsamtools? In particular I see (looking for compilation of faidx.c, and generation of libraries)
and then (looking for compilation of src/fafile.c, and linking to libhts
Having the same issue, just did the suggested ubuntu upgrade, with included a base R upgrade to 3.6.0.
HTSlib version: 1.15.6
Here is the end of the install output with the final error. The whole output is over the character limit, and while there are a couple of warnings in there I suspect that's not where the trouble is.
Can you try the following. This should identify if
faidx_fetch_seq2really is missing from your version of Rhtslib.On my machine (which doesn't produced the error you're seeing) I get:
Having the same issue.
The suggested grep for faidxfetchseq2 gives me:
not a huge help, but getting the same error on 3.6.0.
and the grep gives me the same
tried your commands, got same output as others:
... and the compilation ...
... and the Rsamtools - searched for 'libhts' but seems missing...
...character limit, perhaps e-mail?...
To find references to
libhtsin the installation of Rsamtools you probably need to look for-lhts. This is slightly different from what Martin showed and is due to differences between static and dynamic linking, which is probably a Mac vs Linux thing in this example.Since multiple people are probably interested in getting to the bottom of this email is a bit hard to keep track of, but you can post complete logs to something like https://www.pastebin.com and then provide the link to that.
you can find my full logs here: https://pastebin.com/fNw41s80
likewise here are mine https://pastebin.com/vmpAcLzE
all but one of the warnings are for unused return values, except for this one when it's building tabixfile using htslib as an included library:
Can you install scPipe? This package is also linked to Rhtslib but doesn't depend on Rsamtools and doesn't call
faidx_fetch_seq2. Make sure to install withBiocManager::install("scPipe").But before trying to install any new packages, make sure that
BiocManager::valid()reports a clean installation.H.
after fixing the packages the valid check flagged, the scPipe install died like this:
looks like it depends on a couple of things that depend on Rsamtools. As you would expect from the error message, BiocManager::install("GenomicAlignments") fails when it can't find Rsamtools
Right, scPipe depends on rtracklayer and I forgot that rtracklayer depends on Rsamtools. Sorry for that.
However it seems that, despite rtracklayer being listed in scPipe's Imports field, nothing is imported from rtracklayer. So you should be able to get rid of that dep, at least for the compilation/installation purpose. Can I ask you to try the following:
Then edit
scPipe/DESCRIPTIONto remove rtracklayer. Save. Then:Let us know how that goes.
Thanks, H.
The command to clone is
sorry. (Now corrected in my previous comment.)
ok, went in and deleted rtracklayer from the description file and it installed without a whimper. And then saying library(scPipe) also worked fine.
Puzzling!
Let's try something else. Clone Rsamtools:
Try to install it:
It should fail at the very end with the usual error. Now:
Then show us the output of:
This is what it gives for me:
Thanks!
scPipe without rtracklayer also works perfectly for me.
here is my output of ldd Rsamtools.so after the failed installation: https://pastebin.com/PN3Lmmbv
Thanks!
Interesting. In your output Rsamtools is linking against a system version of htslib, rather than the version installed via Rhtslib. The relevant line is:
and for Hervé it's
Based on this, installing the Ubuntu
libhts-devpackage lets me recreate this error. However for me that entry is:which looks like it should be correct, but still throws the same error. Something in the linking step during compilation is finding things in the wrong order.
Hi, So far I'm having exactly the same issues with Rsamtools as above users. With grep I also got the same error code:
I also tried git installation of scPipe after removing the rtracklayer dependency and it all went well.
My output of ldd Rsamtools.so after failed installation is this: https://pastebin.com/9WRs1eRg
Thanks for your help!
I think I may have tracked this down. Can you please try installing this modified version of Rhtslib and then retrying Rsamtools.
It worked great! Thanks for the help!
Perfect! Thanks a lot for the help!
Also works for me, thank you very much!
cool, all I had to do was install 'remote' and that worked like a charm. Thanks so much for chasing this down.
one thing leads to another, now ggbio installs fine (apparently), but when I try to load it it fails to find faidxfetchseq2 in the Rsamtools library:
Should this go in a different thread, or will this be solved by the updates to Rhtslib?
It's almost certainly related so no need to start a new thread. Did you reinstall ggbio after getting the new Rhtslib? I'll try on my system later.
yeah, looks like it pretty much has to be the same issue, and yes, the ggbio install was after the modified Rhtslib (and successful install of Rsamtools, rtracklayer and ballgown)