无法根据 rtracklayer R3.4.0 安装 R 包
unable to install R packages depending on rtracklayer R3.4.0
我已将 mac 上的 R 更新为 R3.4.0。不幸的是，现在我无法安装任何依赖于 rtracklayer.
的生物导体包
我有 Bioc version 3.5 和 R version 3.4.0
我已经安装了最新版本的 BiocInstaller (v. 1.26.0)。
从 bioc 安装包没有问题，例如 affy、limma 或类似的。但是只要需要 rtracklayer（所有注释包），我就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
我在另一个 post 中发现可以使用 R CMD otool -L path/to/rtrackalyer.so 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)
但是并没有解决问题。
对于解决问题的任何帮助，我将不胜感激。
谢谢
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
我基本上和你在同一个系统上。我最终得到 rtracklayer 加载，但这需要毅力和阅读大量错误消息并等待。挂断是让 Rsamtools 加载，为此我删除了旧的库副本，安装 XCode 命令行工具（因为 XML 出错）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。不确定其中哪一个是解决方案，可能需要其中几个。
我在尝试加载 MetaboSignal Bioconductor 包时遇到了与@AssaYeroslaviz 完全相同的问题，并且还尝试了 post，其中建议更改 CMD otool -L path/to/rtrackalyer.so。但是它没有用，@42-的解决方案也没有用。安装 clang4 和 gfortran 后，正如@42- 在 https://cran.r-project.org/bin/macosx/tools/ 中所建议的那样，我从源代码中安装了 rtrackalyer，而不是在 RStudio 中，而是直接在 RConsole 中。在 RConsole 中加载 rtracklayer 和我需要的包后，重新安装 RStudio 效果很好。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
可能会有用，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")
所以我终于设法解决了我自己的问题。我仍然不确定问题出在哪里。我已经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 包并从本地 tar.gz 文件安装它。
现在它再次运行。真的不知道为什么。
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
我已将 mac 上的 R 更新为 R3.4.0。不幸的是，现在我无法安装任何依赖于 rtracklayer.
我有 Bioc version 3.5 和 R version 3.4.0
我已经安装了最新版本的 BiocInstaller (v. 1.26.0)。
从 bioc 安装包没有问题，例如 affy、limma 或类似的。但是只要需要 rtracklayer（所有注释包），我就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
我在另一个 post 中发现可以使用 R CMD otool -L path/to/rtrackalyer.so 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)
但是并没有解决问题。
对于解决问题的任何帮助，我将不胜感激。
谢谢
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
我基本上和你在同一个系统上。我最终得到 rtracklayer 加载，但这需要毅力和阅读大量错误消息并等待。挂断是让 Rsamtools 加载，为此我删除了旧的库副本，安装 XCode 命令行工具（因为 XML 出错）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。不确定其中哪一个是解决方案，可能需要其中几个。
我在尝试加载 MetaboSignal Bioconductor 包时遇到了与@AssaYeroslaviz 完全相同的问题，并且还尝试了 post，其中建议更改 CMD otool -L path/to/rtrackalyer.so。但是它没有用，@42-的解决方案也没有用。安装 clang4 和 gfortran 后，正如@42- 在 https://cran.r-project.org/bin/macosx/tools/ 中所建议的那样，我从源代码中安装了 rtrackalyer，而不是在 RStudio 中，而是直接在 RConsole 中。在 RConsole 中加载 rtracklayer 和我需要的包后，重新安装 RStudio 效果很好。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
可能会有用，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")
所以我终于设法解决了我自己的问题。我仍然不确定问题出在哪里。我已经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 包并从本地 tar.gz 文件安装它。
现在它再次运行。真的不知道为什么。
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