在 conda 环境中将 rtracklayer 包从 Bioconductor 加载到 R 时，分段错误和内存未映射
segmentation fault and memory not mapped when loading the rtracklayer package from Bioconductor into R in a conda environment
我已经创建了一个包含 r 和 bioconductor-rtracklayer 的 conda 环境：
conda create --name bioconductor-rtracklayer --channel conda-forge --channel bioconda --channel r --yes r=3.5.1 bioconductor-rtracklayer=1.42.1
并激活它：
conda activate bioconductor-rtracklayer
我正在使用 macOS High Sierra 10.13.3
然后我在终端中打开 R 并输入：
library(rtracklayer)
并得到以下错误：
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, 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)})
8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
11: .getRequiredPackages2(pkgInfo, quietly = quietly)
12: library(rtracklayer)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
我不明白问题出在哪里。有人可以帮助我吗？
请注意，我可以 运行 library(rtracklayer) 从 RStudio 中毫无问题地使用包中的函数。为什么命令行和 RStudio 之间存在这种差异？
根据 Johannes Koester 的评论，我创建了一个 conda 环境并安装了 bioconductor-rtracklayer，但未指定 r 通道：
conda create --name bioconductor-rtracklayer --channel conda-forge --channel bioconda --yes r=3.5.1 bioconductor-rtracklayer=1.42.1
激活环境，在终端中打开R并输入library(rtracklayer)但我仍然得到以下错误：
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, 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)})
8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
11: .getRequiredPackages2(pkgInfo, quietly = quietly)
12: library(rtracklayer)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
R is aborting now ...
[1] 44550 segmentation fault R
请注意，我的 .libPaths() 包含：
.libPaths()
[1] "/Users/user/Library/R/3.5/library"
[2] "/Users/user/anaconda/envs/bioconductor-rtracklayer/lib/R/library"
我是否应该删除 .libPaths() 中的第一行以便 R 在 conda 环境中获取 R 包？
然而，library(rtracklayer, lib.loc = '/Users/user/anaconda/envs/bioconductor-rtracklayer/lib/R/library') 给了我同样的错误。
conda forge和bioconda不需要混用r通道。它们甚至是二进制不兼容的。来自 r 频道的所有包现在都在 conda-forge 中。请参阅 http://bioconda.github.io 了解正确的频道顺序和组合。希望这可能已经解决了错误。
进入 .bash_profile 并删除了 R_LIBS_USER 变量。它现在正在工作。由 Johannes Koester 建议。
我已经创建了一个包含 r 和 bioconductor-rtracklayer 的 conda 环境：
conda create --name bioconductor-rtracklayer --channel conda-forge --channel bioconda --channel r --yes r=3.5.1 bioconductor-rtracklayer=1.42.1
并激活它：
conda activate bioconductor-rtracklayer
我正在使用 macOS High Sierra 10.13.3
然后我在终端中打开 R 并输入：
library(rtracklayer)
并得到以下错误：
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, 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)})
8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
11: .getRequiredPackages2(pkgInfo, quietly = quietly)
12: library(rtracklayer)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
我不明白问题出在哪里。有人可以帮助我吗？
请注意，我可以 运行 library(rtracklayer) 从 RStudio 中毫无问题地使用包中的函数。为什么命令行和 RStudio 之间存在这种差异？
根据 Johannes Koester 的评论，我创建了一个 conda 环境并安装了 bioconductor-rtracklayer，但未指定 r 通道：
conda create --name bioconductor-rtracklayer --channel conda-forge --channel bioconda --yes r=3.5.1 bioconductor-rtracklayer=1.42.1
激活环境，在终端中打开R并输入library(rtracklayer)但我仍然得到以下错误：
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, 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)})
8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
11: .getRequiredPackages2(pkgInfo, quietly = quietly)
12: library(rtracklayer)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
R is aborting now ...
[1] 44550 segmentation fault R
请注意，我的 .libPaths() 包含：
.libPaths()
[1] "/Users/user/Library/R/3.5/library"
[2] "/Users/user/anaconda/envs/bioconductor-rtracklayer/lib/R/library"
我是否应该删除 .libPaths() 中的第一行以便 R 在 conda 环境中获取 R 包？
然而，library(rtracklayer, lib.loc = '/Users/user/anaconda/envs/bioconductor-rtracklayer/lib/R/library') 给了我同样的错误。
conda forge和bioconda不需要混用r通道。它们甚至是二进制不兼容的。来自 r 频道的所有包现在都在 conda-forge 中。请参阅 http://bioconda.github.io 了解正确的频道顺序和组合。希望这可能已经解决了错误。
进入 .bash_profile 并删除了 R_LIBS_USER 变量。它现在正在工作。由 Johannes Koester 建议。