Question

我已在我的Mac上将R更新为R3.4.0。不幸的是，现在我无法安装任何取决于rtracklayer的生物导体包。

我有Bioc version 3.5和R version 3.4.0 我安装了最新版本的BiocInstaller（v.1.26.0）。从bioc安装包装没有问题，例如affy，limma或类似物。但是，如果需要rtracklayer（所有注释包），我会收到以下错误消息：

> biocLite("BSgenome.Rnorvegicus.UCSC.rn5")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘BSgenome.Rnorvegicus.UCSC.rn5’
installing the source package ‘BSgenome.Rnorvegicus.UCSC.rn5’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz'
Content type 'application/x-gzip' length 614635033 bytes (586.2 MB)
==================================================
downloaded 586.2 MB

* installing *source* package ‘BSgenome.Rnorvegicus.UCSC.rn5’ ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
  Reason: image not found
Error : package ‘rtracklayer’ could not be loaded
ERROR: lazy loading failed for package ‘BSgenome.Rnorvegicus.UCSC.rn5’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BSgenome.Rnorvegicus.UCSC.rn5’

The downloaded source packages are in
    ‘/private/var/folders/sh/kwc66sqn4x36cjf9vncy99xm0000gp/T/RtmpX7Ltad/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome.Rnorvegicus.UCSC.rn5’ had non-zero exit status

我在另一篇文章中发现，使用R CMD otool -L path / to / rtrackalyer.so可以设置rtracklayer.so的路径。我也试过了。

R CMD otool -L /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so:
    rtracklayer.so (compatibility version 0.0.0, current version 0.0.0)
    /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
    /usr/local/opt/openssl/lib/libssl.1.0.0.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib (compatibility version 1.0.0, current version 1.0.0)
    /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libR.dylib (compatibility version 3.4.0, current version 3.4.0)
    /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1259.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)

但它没有解决问题。

我很感激任何帮助解决问题。

由于

阿萨

> R.version
               _                           
platform       x86_64-apple-darwin15.6.0   
arch           x86_64                      
os             darwin15.6.0                
system         x86_64, darwin15.6.0        
status                                     
major          3                           
minor          4.0                         
year           2017                        
month          04                          
day            21                          
svn rev        72570                       
language       R                           
version.string R version 3.4.0 (2017-04-21)
nickname       You Stupid Darkness  

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] biomaRt_2.32.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10         IRanges_2.10.0       XML_3.98-1.7         digest_0.6.12       
 [5] bitops_1.0-6         DBI_0.6-1            stats4_3.4.0         RSQLite_1.1-2       
 [9] S4Vectors_0.14.0     tools_3.4.0          Biobase_2.36.0       RCurl_1.95-4.8      
[13] parallel_3.4.0       compiler_3.4.0       BiocGenerics_0.22.0  AnnotationDbi_1.38.0
[17] memoise_1.1.0

Answer 1

我基本上和你在同一个系统上。我最终加载了rtracklayer，但它需要坚持不懈并阅读大量错误消息并等待。挂起是为了加载Rsamtools，为此我删除了旧的库副本，安装了XCode命令行工具（由于XML的错误）并在重新启动后重新加载source("https://bioconductor.org/biocLite.R")。我还按照https://cran.r-project.org/bin/macosx/tools/安装了clang4。不确定这些是哪种解决方案，并且可能需要其中一些解决方案。

Answer 2

在尝试加载MetaboSignal Bioconductor软件包时遇到与@AssaYeroslaviz完全相同的问题，并尝试了建议更改CMD otool -L path/to/rtrackalyer.so的帖子。然而它没有用，也没有@ 42-的解决方案。安装clang4和gfortran后，按照@ {42- https://cran.r-project.org/bin/macosx/tools/的建议，我从源代码中安装rtrackalyer而不是在RStudio中，而是直接安装在RConsole中。加载rtracklayer和我在RConsole中需要的包后，重新安装RStudio运行良好。我使用的代码：

     library("BiocInstaller")
     biocLite("rtracklayer", type="source")
     library("rtracklayer")

sessionInfo（）

     R version 3.4.0 (2017-04-21)
     Platform: x86_64-apple-darwin15.6.0 (64-bit)
     Running under: macOS Sierra 10.12.4

     Matrix products: default
              BLAS:/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
     LAPACK:/Frameworks/R.framework/Versions/3.4/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] parallel  stats4    stats     graphics  grDevices utils              datasets  methods   base     

     other attached packages:
     [1] rtracklayer_1.36.0   GenomicRanges_1.28.1 GenomeInfoDb_1.12.0           IRanges_2.10.0       S4Vectors_0.14.0     BiocGenerics_0.22.0           BiocInstaller_1.26.0

     loaded via a namespace (and not attached):
      [1] XVector_0.16.0             zlibbioc_1.22.0                     GenomicAlignments_1.12.0   BiocParallel_1.10.1        lattice_0.20-35                     tools_3.4.0               
      [7] SummarizedExperiment_1.6.1 grid_3.4.0                          Biobase_2.36.2             matrixStats_0.52.2         Matrix_1.2-10                       GenomeInfoDbData_0.99.0   
     [13] bitops_1.0-6               RCurl_1.95-4.8                      DelayedArray_0.2.0         compiler_3.4.0             Biostrings_2.44.0                   Rsamtools_1.28.0          
     [19] XML_3.98-1.7

可能有用，traceback()

     6: stop(msg, call. = FALSE, domain = NA)
     5: value[[3L]](cond)
     4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     3: tryCatchList(expr, classes, parentenv, handlers)
     2: 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)
        })
     1: library("rtracklayer")

Answer 3

所以我终于设法解决了自己的问题。我仍然不确定问题是什么。我重新安装了最新版本的R（3.4.0）/ bioC（3.5）和RStudio（1.0.143）。之后我下载了rtracklayer软件包并从当地的tar.gz文件安装了它。

现在再次运行。不知道为什么。

R.version                  _
  平台x86_64-apple-darwin15.6.0
  拱x86_64
  os darwin15.6.0
  system x86_64，darwin15.6.0
  状态
  专业3   小4.0   2017年
年   月04日   第21天   svn rev 72570
  语言R
  version.string R版本3.4.0（2017-04-21）   昵称你愚蠢的黑暗

根据rtracklayer R3.4.0无法安装R软件包

3 个答案: