無法安裝R軟件包，具體取決於rtracklayer R3.4.0

Question

我已經在Mac上將R更新為R3.4.0。 不幸的是，現在我無法安裝依賴於任何Bioconductor的包rtracklayer 。

我有Bioc version 3.5和R version 3.4.0我已經安裝了最新版本的BiocInstaller （v。1.26.0）。 從仿生安裝軟件包（例如，affy，limma或類似文件）沒有問題。 但是只要需要rtracklayer（所有注釋包），我就會收到以下錯誤消息：

> 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

我在另一篇文章中發現，可以使用R CMD otool -L path / to / rtrackalyer.so來設置rtracklayer.so的路徑。 我也嘗試過

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)

但這並不能解決問題。

對於解決問題，我將不勝感激。

謝謝

阿薩

> 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

我基本上和您在同一系統上。 我最終讓rtracklayer加載，但是它需要毅力並需要閱讀大量錯誤消息並等待。 掛起的原因是要加載Rsamtools，為此，我刪除了舊的庫副本，安裝了XCode命令行工具（由於XML錯誤），並在重新啟動后重新加載了source("https://bioconductor.org/biocLite.R") 。 我還按照以下方式安裝了clang4： https://cran.r-project.org/bin/macosx/tools/ ://cran.r-project.org/bin/macosx/tools/。 不知道這些解決方案是什么，可能有幾個需要。

Answer 2

嘗試加載MetaboSignal Bioconductor軟件包時，我遇到了與@AssaYeroslaviz完全相同的麻煩，並且還嘗試了建議更改CMD otool -L path/to/rtrackalyer.so 。 但是它沒有用，@ 42-也沒有解決方案。 按照@ 42-在https://cran.r-project.org/bin/macosx/tools/中建議的那樣安裝clang4和gfortran后，我從源代碼而不是RStudio中而是直接在RConsole中安裝了rtrackalyer 。 加載rtracklayer和rtracklayer的軟件包后，重新安裝RStudio效果很好。 我使用的代碼：

     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

traceback()可能有用

     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

所以我終於設法解決了自己的問題。 我仍然不確定是什么問題。 我已經重新安裝了R（3.4.0）/ bioC（3.5）和RStudio（1.0.143）的最新版本。 之后，我下載了rtracklayer軟件包並從一個有效的本地tar.gz文件中安裝了它。

現在，它再次運行。 真的不知道為什么。

R.版本_
平台x86_64-apple-darwin15.6.0
拱x86_64
操作系統darwin15.6.0
系統x86_64，darwin15.6.0
狀態
專業3
小4.0
年2017
第04個月
第21天
svn版本72570
語言R
version.string R版本3.4.0（2017-04-21）昵稱You Stupid Darkness