我用r和bioconductor-rtracklayer创建了一个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
我正在研究macOS High Sierra 10.13.3
然后我在终端打开R并键入：
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:
我不明白问题是什么。请有人帮帮我吗？
请注意，我可以从RStudio中运行library(rtracklayer)而没有任何问题，我可以成功使用包中的函数。为什么命令行和RStudio之间存在这种差异？
conda create --name bioconductor-rtracklayer --channel conda-forge --channel bioconda --yes r=3.5.1 bioconductor-rtracklayer=1.42.1
激活环境，在终端打开R并输入library(rtracklayer)但我仍然遇到以下错误：
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"
我应该删除.libPaths()里面的第一行R来获取conda环境中的R包吗？
但是，library(rtracklayer, lib.loc = '/Users/user/anaconda/envs/bioconductor-rtracklayer/lib/R/library')给了我同样的错误。
没有必要将r通道与conda forge和bioconda混合使用。它们甚至是二进制不兼容的。来自r频道的所有套餐现在都是conda-forge。请参阅http://bioconda.github.io获取正确的渠道订单和组合。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。它现在正在运作。 Johannes Koester建议。