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immunogenomics
Error installing harmony in R
Hello.
I am having problems installing harmony and I get the following error. I updated my R by downloading the pkg from CRAN and then manually re-installing all the packages I needed. Have not had any issues with other GitHub packages that I was installing. My sessionInfo() is included below too.
> library(devtools)
Loading required package: usethis
> install_github("immunogenomics/harmony")
Downloading GitHub repo immunogenomics/harmony@HEAD
✓ checking for file ‘/private/var/folders/tn/9np01dtn13dgk_k10m3f92j80000gp/T/RtmpwyRbTN/remotes20a159c14d2b/immunogenomics-harmony-88b1e2a/DESCRIPTION’ ...
─ preparing ‘harmony’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘harmony_1.0.tar.gz’
* installing *source* package ‘harmony’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c harmony.cpp -o harmony.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o harmony.so RcppExports.o harmony.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-harmony/00new/harmony/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
sh: line 1: 8448 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/tn/9np01dtn13dgk_k10m3f92j80000gp/T//RtmpOunzZq/file20e64b206157'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/harmony’
Error: Failed to install 'harmony' from GitHub:
(converted from warning) installation of package ‘/var/folders/tn/9np01dtn13dgk_k10m3f92j80000gp/T//RtmpwyRbTN/file20a1835c5a2/harmony_1.0.tar.gz’ had non-zero exit status
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.3.1 usethis_1.6.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.11 magrittr_1.5 pkgload_1.1.0 R6_2.4.1 rlang_0.4.7
[6] fansi_0.4.1 tools_4.0.2 pkgbuild_1.1.0 xfun_0.16 sessioninfo_1.1.1
[11] tinytex_0.25 cli_2.0.2 withr_2.2.0 ellipsis_0.3.1 remotes_2.2.0
[16] assertthat_0.2.1 digest_0.6.25 rprojroot_1.3-2 crayon_1.3.4 processx_3.4.3
[21] callr_3.4.3 fs_1.4.2 ps_1.3.3 curl_4.3 testthat_2.3.2
[26] memoise_1.1.0 glue_1.4.1 compiler_4.0.2 desc_1.2.0 backports_1.1.8
[31] prettyunits_1.1.1
Dear Harmony team, I am also having an issue installing harmony after transitioning to R 4.0.1.
sh: line 1: 196346 Segmentation fault R_TESTS= '/pstore/apps/R/4.0.1-foss-2018b/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpmKjbQn/file2fd60337a9c42'
*** caught segfault ***
address 0x20, cause 'memory not mapped'
Traceback:
1: Module(module, mustStart = TRUE, where = env)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e)
6: loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow = TRUE)
7: (function (ns) loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow = TRUE))(<environment>)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch((function (ns) loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow = TRUE))(<environment>), error = function(e) e)
12: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e), list(FUN = f, WHERE = where)), where)
13: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e), list(FUN = f, WHERE = where)), where)
14: .doLoadActions(where, attach)
15: methods::cacheMetaData(ns, TRUE, ns)
16: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
17: asNamespace(ns)
18: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
19: loadNamespace(name)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(loadNamespace(name), error = function(e) { warning(gettextf("namespace %s is not available and has been replaced\nby .GlobalEnv when processing object %s", sQuote(name)[1L], sQuote(where)), domain = NA, call. = FALSE, immediate. = TRUE) .GlobalEnv})
24: ..getNamespace(c("Seurat", "3.0.0"), "cell_lines_small_seurat_v3")
25: load(zfile, envir = tmp_env)
26: utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv)
27: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
28: suppressWarnings(utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv))
29: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
30: suppressMessages(suppressWarnings(utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv)))
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(suppressMessages(suppressWarnings(utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv))), error = identity)
35: list_data_in_pkg(dataDir = dataDir)
36: .build_data_index(dataDir, contents)
37: saveRDS(.build_data_index(dataDir, contents), file.path(outDir, "Meta", "data.rds"))
38: .install_package_Rd_indices(dir, outDir)
39: tools:::.install_package_indices(".", "/pstore/home/tosevskv/R/x86_64-pc-linux-gnu-library/4.0.1-foss/00LOCK-harmony/00new/harmony")
An irrecoverable exception occurred. R is aborting now ...
ERROR: installing package indices failed
* removing ‘/pstore/home/tosevskv/R/x86_64-pc-linux-gnu-library/4.0.1-foss/harmony’
Is there a way around this? Is the fault with harmony or my cluster?
Thanks, Vinko
Good morning everyone :)
I am having similar issues:
> library(devtools)
Loading required package: usethis
> install_github("immunogenomics/harmony")
Downloading GitHub repo immunogenomics/harmony@HEAD
checking DESCRIPTION meta-information ...f/mxk7z9d93s97hygvdgh66knh5tlp8z/T/Rtmp2NWN4D/remotes7f0e32126d68/immunogenomics-harmony-88b1e2a/DESCRIPTION’ ...
Installing package into ‘/Users/milanezdelimap/Library/R/4.0/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘harmony’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/milanezdelimap/Library/R/4.0/library/Rcpp/include' -I'/Users/milanezdelimap/Library/R/4.0/library/RcppArmadillo/include' -I'/Users/milanezdelimap/Library/R/4.0/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/milanezdelimap/Library/R/4.0/library/Rcpp/include' -I'/Users/milanezdelimap/Library/R/4.0/library/RcppArmadillo/include' -I'/Users/milanezdelimap/Library/R/4.0/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c harmony.cpp -o harmony.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o harmony.so RcppExports.o harmony.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/milanezdelimap/Library/R/4.0/library/00LOCK-harmony/00new/harmony/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
sh: line 1: 32653 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/1f/mxk7z9d93s97hygvdgh66knh5tlp8z/T//RtmpFCXLJw/file7f581c51094b'
ERROR: installing package indices failed
* removing ‘/Users/milanezdelimap/Library/R/4.0/library/harmony’
Error: Failed to install 'harmony' from GitHub:
(converted from warning) installation of package ‘/var/folders/1f/mxk7z9d93s97hygvdgh66knh5tlp8z/T//Rtmp2NWN4D/file7f0e4af6bfa1/harmony_1.0.tar.gz’ had non-zero exit status
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.3.2 usethis_1.6.3
loaded via a namespace (and not attached):
[1] magrittr_1.5 pkgload_1.1.0 R6_2.4.1 rlang_0.4.7 fansi_0.4.1 tools_4.0.2 pkgbuild_1.1.0 sessioninfo_1.1.1 cli_2.0.2 withr_2.3.0 ellipsis_0.3.1
[12] remotes_2.2.0 assertthat_0.2.1 digest_0.6.25 rprojroot_1.3-2 crayon_1.3.4 processx_3.4.4 callr_3.4.4 fs_1.5.0 ps_1.3.4 curl_4.3 testthat_2.3.2
[23] memoise_1.1.0 glue_1.4.2 compiler_4.0.2 desc_1.2.0 backports_1.1.10 prettyunits_1.1.1
$ gfortran --version
GNU Fortran (GCC) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
i finished it: R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-conda_cos6-linux-gnu (64-bit)
library(harmony) packageVersion('harmony') [1] ‘1.0’
by: wget https://github.com/immunogenomics/harmony/archive/master.zip # or download by webpage library(devtools) install_local('yourpath/harmony-master.zip')
good luck to you !!!
Thanks for your comment! All three comments above use R4 though, while you are on R3. Hope Harmony will get implemented in R4 as well.