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Azimuth installation error #241

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gevro opened this issue Oct 18, 2024 · 1 comment
Open

Azimuth installation error #241

gevro opened this issue Oct 18, 2024 · 1 comment

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@gevro
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gevro commented Oct 18, 2024

Hi,
I'm getting the below error:

* installing *source* package ‘Azimuth’ ...
** using staged installation
** libs
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/gpfs/data/lab/bin/R-conda/lib/R/include" -DNDEBUG  -I'/gpfs/data/lab/bin/R-conda/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /gpfs/data/lab/bin/R-conda/include -I/gpfs/data/lab/bin/R-conda/include -Wl,-rpath-link,/gpfs/data/lab/bin/R-conda/lib   -fpic  -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /gpfs/data/lab/bin/R-conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1710256485633/work=/usr/local/src/conda/r-base-4.2.3 -fdebug-prefix-map=/gpfs/data/lab/bin/R-conda=/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/gpfs/data/lab/bin/R-conda/lib/R/include" -DNDEBUG  -I'/gpfs/data/lab/bin/R-conda/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /gpfs/data/lab/bin/R-conda/include -I/gpfs/data/lab/bin/R-conda/include -Wl,-rpath-link,/gpfs/data/lab/bin/R-conda/lib   -fpic  -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /gpfs/data/lab/bin/R-conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1710256485633/work=/usr/local/src/conda/r-base-4.2.3 -fdebug-prefix-map=/gpfs/data/lab/bin/R-conda=/usr/local/src/conda-prefix  -c csc_to_csr.cpp -o csc_to_csr.o
x86_64-conda-linux-gnu-c++ -std=gnu++11 -shared -L/gpfs/data/lab/bin/R-conda/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/gpfs/data/lab/bin/R-conda/lib -Wl,-rpath-link,/gpfs/data/lab/bin/R-conda/lib -L/gpfs/data/lab/bin/R-conda/lib -o Azimuth.so RcppExports.o csc_to_csr.o -L/gpfs/data/lab/bin/R-conda/lib/R/lib -lR
installing to /gpfs/data/lab/bin/R-conda/lib/R/library/00LOCK-Azimuth/00new/Azimuth/libs
** R
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 3315480 Segmentation fault      (core dumped) R_TESTS= '/gpfs/data/lab/bin/R-conda/lib/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpjMovP0/file32970370b7ec1b'

 *** caught segfault ***
address 0x155542eab170, cause 'invalid permissions'

Traceback:
 1: fun(libname, pkgname)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch(fun(libname, pkgname), error = identity)
 6: runHook(".onLoad", env, package.lib, package)
 7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 8: asNamespace(ns)
 9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
10: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
11: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
12: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
13: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
14: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
15: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
16: loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source,     keep.parse.data = keep.parse.data, partial = TRUE)
17: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
18: suppressPackageStartupMessages(loadNamespace(package = package,     lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data,     partial = TRUE))
19: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,     keep.parse.data = keep.parse.data, compress = compress, set.install.dir = set.install.dir)
20: tools:::makeLazyLoading("Azimuth", "/gpfs/data/lab/bin/R-conda/lib/R/library/00LOCK-Azimuth/00new",     keep.source = FALSE, keep.parse.data = FALSE, set.install.dir = "/gpfs/data/lab/bin/R-conda/lib/R/library/Azimuth")
An irrecoverable exception occurred. R is aborting now ...
ERROR: lazy loading failed for package ‘Azimuth’
* removing ‘/gpfs/data/lab/bin/R-conda/lib/R/library/Azimuth’
* restoring previous ‘/gpfs/data/lab/bin/R-conda/lib/R/library/Azimuth’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpoYTq5f/file3284454d7a2c9c/Azimuth_0.5.0.tar.gz’ had non-zero exit status
@Linpu2023
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Having the same problem here...I am using MacOS, Rstudio version 2024.09.1+394. Tried remotes::, Bioconductor, neither worked

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