Comments (3)
Hi @vjbaskar !
Could you paste the exact error you are getting (the whole output when you are trying to install it).
Thanks!
from cistopic.
Hi @cbravo93,
It is part of my docker container that I run using Singularity in our HPC. It installs fine, no problem there. When I load the library it gives the error below.
Error: package or namespace load failed for ‘cisTopic’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/library/float/libs/float.so':
libgfortran.so.3: cannot open shared object file: No such file or directory
Traceback:
1. library(cisTopic)
2. tryCatch({
. attr(package, "LibPath") <- which.lib.loc
. ns <- loadNamespace(package, lib.loc)
. env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
. }, error = function(e) {
. P <- if (!is.null(cc <- conditionCall(e)))
. paste(" in", deparse(cc)[1L])
. else ""
. msg <- gettextf("package or namespace load failed for %s%s:\n %s",
. sQuote(package), P, conditionMessage(e))
. if (logical.return)
. message(paste("Error:", msg), domain = NA)
. else stop(msg, call. = FALSE, domain = NA)
. })
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value[[3L]](cond)
6. stop(msg, call. = FALSE, domain = NA)
So when print its shared lib dependencies, I get this
Singularity> ldd /usr/local/lib/R/library/float/libs/float.so
linux-vdso.so.1 (0x00007ffea67ea000)
libRlapack.so => /usr/local/lib/R/lib/libRlapack.so (0x00002ac831a37000)
libRblas.so => /usr/local/lib/R/lib/libRblas.so (0x00002ac831c27000)
libgfortran.so.3 => not found
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002ac831c5d000)
libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002ac831dac000)
libR.so => /usr/local/lib/R/lib/libR.so (0x00002ac831df6000)
libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00002ac8322a8000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00002ac8322ea000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002ac83230d000)
libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5 (0x00002ac8324ff000)
/lib64/ld-linux-x86-64.so.2 (0x00002ac831847000)
libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8 (0x00002ac8327c7000)
libpcre2-8.so.0 => /lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00002ac832817000)
liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00002ac8328a9000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00002ac8328d2000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00002ac8328e5000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002ac832901000)
libicuuc.so.66 => /lib/x86_64-linux-gnu/libicuuc.so.66 (0x00002ac832907000)
libicui18n.so.66 => /lib/x86_64-linux-gnu/libicui18n.so.66 (0x00002ac832aed000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002ac832dee000)
libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6 (0x00002ac832e09000)
libicudata.so.66 => /lib/x86_64-linux-gnu/libicudata.so.66 (0x00002ac832e39000)
libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00002ac8348fa000)
This may as well be an error due to containerisation + singularity + R combination but I have no way of testing this independently elsewhere.
Many thanks
Vijay
from cistopic.
Hi!
Can you check if you actually have gfortran in your image (locate gfortran)?
Normally I work with a conda R environment in HPC, that does not give issues so far.
Cheers!
C
from cistopic.
Related Issues (20)
- possibility to use BAM files from bulk ChIP HOT 1
- annotateRegions with own dataset HOT 1
- createcisTopicObject and genomic coordinates incompatibility error HOT 3
- input from fragments.tsv.gz? HOT 1
- Installation issue HOT 2
- Tutorial Dataset files HOT 1
- tSNE Clustering Thresholds HOT 1
- LDA run with Python and LogLikelihhod HOT 1
- How can I run cisTopic in R 4.0 HOT 2
- Ununsed Arguement error in cisTopic/TcisTarget HOT 1
- cisTopicObject <- selectModel(cisTopicObject) Error in .Call("rs_createGD") : C symbol name "rs_createGD" not in load table HOT 1
- Unused argument error while running topicsRcisTarget
- add cisTopic output to Seurat object? HOT 1
- Running Cistopic HOT 1
- Installation error "Failed to install 'unknown package' from Github: ..." HOT 1
- Loading Multiome data
- sha256sum download failed HOT 1
- Error in metadataFeather(path) : Invalid: Not a feather file HOT 3
- Missing resource cleanup in runWarpLDAModels
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cistopic.