无法加载R DESeq2库，安装所有丢失的软件包并仍然存在问题

时间：2016-09-12 09:28:33

标签： r bioinformatics bioconductor install.packages

我在为R安装和使用DESeq2软件包时遇到了一些不好的问题。

我在Win7上新安装了R 3.3.1和Rstudio 0.99.903。 我尝试使用：

安装DESeq2 
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

但是它遇到了很多错误（某些依赖包的一些缺失包等...）然后我尝试通过从CREN下载并从.zip文件安装缺少的包来手动安装所有缺少的包。

然后我尝试运行几个命令，我希望他们的信息有助于找到所有错误的原因： 首先是biocLite（所有相关软件包的安装程序，在之前安装的DESeq2软件包上一切都很顺利......但它是在Linux上）

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'survival'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
              binary source needs_compilation
GenomicRanges 1.24.2 1.24.3              TRUE

  Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘lattice’ ‘mgcv’ ‘survival’
  These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'survival'
Update all/some/none? [a/s/n]: 
n
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘DESeq2’
also installing the dependency ‘Rcpp’


  There is a binary version available but the source version is later:
       binary source needs_compilation
Rcpp 0.12.4.5 0.12.7              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/DESeq2_1.12.4.zip'
Content type 'application/zip' length 3937521 bytes (3.8 MB)
downloaded 3.8 MB

package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'Rcpp', 'survival'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
                binary source needs_compilation
GenomicRanges   1.24.2 1.24.3              TRUE
Rcpp          0.12.4.5 0.12.7              TRUE

  Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘lattice’ ‘mgcv’ ‘survival’
  These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB

trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages

然后尝试使用biocLite安装DESeq2软件包（看起来一切都很好）

> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘DESeq2’
also installing the dependency ‘Rcpp’


  There is a binary version available but the source version is later:
       binary source needs_compilation
Rcpp 0.12.4.5 0.12.7              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/DESeq2_1.12.4.zip'
Content type 'application/zip' length 3937521 bytes (3.8 MB)
downloaded 3.8 MB

package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'Rcpp', 'survival'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
                binary source needs_compilation
GenomicRanges   1.24.2 1.24.3              TRUE
Rcpp          0.12.4.5 0.12.7              TRUE

  Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘lattice’ ‘mgcv’ ‘survival’
  These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB

trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages

现在加载DESeq2库（错误...）：

> library("DESeq2")
Loading required package: S4Vectors
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, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unsplit


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘data.table’
Error: package or namespace load failed for ‘DESeq2’

尝试安装缺少的包：

> install.packages('data.table', dependencies = TRUE)
also installing the dependencies ‘minqa’, ‘nloptr’, ‘RcppEigen’, ‘lme4’, ‘SparseM’, ‘pbkrtest’, ‘quantreg’, ‘mime’, ‘bit’, ‘gtools’, ‘car’, ‘markdown’, ‘yaml’, ‘bdsmatrix’, ‘sandwich’, ‘lmtest’, ‘chron’, ‘testthat’, ‘hexbin’, ‘fastmatch’, ‘xts’, ‘bit64’, ‘gdata’, ‘caret’, ‘knitr’, ‘curl’, ‘zoo’, ‘plm’

Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘minqa’ ‘nloptr’ ‘RcppEigen’ ‘lme4’ ‘SparseM’ ‘quantreg’ ‘mime’ ‘bit’ ‘gtools’ ‘markdown’
  ‘yaml’ ‘bdsmatrix’ ‘lmtest’ ‘chron’ ‘testthat’ ‘hexbin’ ‘fastmatch’ ‘xts’ ‘bit64’ ‘caret’
  ‘curl’ ‘zoo’ ‘data.table’
  These will not be installed
installing the source packages ‘pbkrtest’, ‘car’, ‘sandwich’, ‘gdata’, ‘knitr’, ‘plm’

trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
Content type 'application/x-gzip' length 165269 bytes (161 KB)
downloaded 161 KB

trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
Content type 'application/x-gzip' length 622922 bytes (608 KB)
downloaded 608 KB

trying URL 'https://cran.rstudio.com/src/contrib/sandwich_2.3-4.tar.gz'
Content type 'application/x-gzip' length 466729 bytes (455 KB)
downloaded 455 KB

trying URL 'https://cran.rstudio.com/src/contrib/gdata_2.17.0.tar.gz'
Content type 'application/x-gzip' length 1041264 bytes (1016 KB)
downloaded 1016 KB

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.14.tar.gz'
Content type 'application/x-gzip' length 1017858 bytes (994 KB)
downloaded 994 KB

trying URL 'https://cran.rstudio.com/src/contrib/plm_1.5-12.tar.gz'
Content type 'application/x-gzip' length 1246790 bytes (1.2 MB)
downloaded 1.2 MB

ERROR: dependency 'lme4' is not available for package 'pbkrtest'
* removing 'C:/Program Files/R/R-3.3.1/library/pbkrtest'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/pbkrtest_0.4-6.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency 'zoo' is not available for package 'sandwich'
* removing 'C:/Program Files/R/R-3.3.1/library/sandwich'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/sandwich_2.3-4.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘sandwich’ had non-zero exit status
ERROR: dependency 'gtools' is not available for package 'gdata'
* removing 'C:/Program Files/R/R-3.3.1/library/gdata'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/gdata_2.17.0.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘gdata’ had non-zero exit status
ERROR: dependencies 'markdown', 'yaml' are not available for package 'knitr'
* removing 'C:/Program Files/R/R-3.3.1/library/knitr'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/knitr_1.14.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘knitr’ had non-zero exit status
ERROR: dependencies 'pbkrtest', 'quantreg' are not available for package 'car'
* removing 'C:/Program Files/R/R-3.3.1/library/car'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/car_2.1-3.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status
ERROR: dependencies 'bdsmatrix', 'zoo', 'sandwich', 'car', 'lmtest' are not available for package 'plm'
* removing 'C:/Program Files/R/R-3.3.1/library/plm'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/plm_1.5-12.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘plm’ had non-zero exit status

The downloaded source packages are in
    ‘C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages’

和sessioninfo：

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255    LC_MONETARY=Hebrew_Israel.1255
[4] LC_NUMERIC=C                   LC_TIME=Hebrew_Israel.1255    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SummarizedExperiment_1.2.3 Biobase_2.32.0             GenomicRanges_1.24.2      
[4] GenomeInfoDb_1.8.7         IRanges_2.6.1              S4Vectors_0.10.3          
[7] BiocGenerics_0.18.0        BiocInstaller_1.22.3      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4.5       Formula_1.2-1       cluster_2.0.4       XVector_0.12.1      splines_3.3.1      
 [6] zlibbioc_1.18.0     munsell_0.4.3       BiocParallel_1.6.6  colorspace_1.2-6    lattice_0.20-33    
[11] plyr_1.8.4          tools_3.3.1         nnet_7.3-12         grid_3.3.1          gtable_0.2.0       
[16] latticeExtra_0.6-28 survival_2.39-4     Matrix_1.2-7.1      gridExtra_2.2.1     RColorBrewer_1.1-2 
[21] ggplot2_2.1.0       acepack_1.3-3.3     rpart_4.1-10        scales_0.4.0        foreign_0.8-66     
>

因为我已经手动安装了＆gt; 10个软件包，所以我认为解决方案不是继续安装缺少的软件包，因为这些软件包会有更多缺少的软件包，而且越来越多，我不会退出这个循环。

我也尝试过在google上找到的东西：

remove.packages(c("ggplot2", "data.table"))
install.packages('Rcpp', dependencies = TRUE)
install.packages('ggplot2', dependencies = TRUE)

但安装也有错误，如果需要，我可以在这里写。

我希望你能看到我能看到并帮助我解决这个问题的东西。

感谢。

3 个答案:

答案 0 :(得分：3)

似乎很多软件包，最重要的是data.table和lme4，都没有正确编译。

我建议安装data.table，lme4以及Packages which are only available in source form, and may need compilation of C/C++/Fortran:与pacman所说的2个语句中表示的所有软件包，然后重新运行Bioconductor安装你的目标包。

install.packages("pacman")
pacman::p_load(data.table, lme4, lattice, mgcv, survival, zoo, markdown,... <etc>)
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

我刚刚确认这适用于Windows。

但请注意，过去因镜像中断而导致的has been associated错误。 因此，如果您仍然遇到此错误，请尝试更改您的CRAN镜像。 install.packages('<package_name>', repo='http://nbcgib.uesc.br/mirrors/cran/')

还要确保已安装并运行RTools.exe。

答案 1 :(得分：1)

biocLite()，install.packages()（和devtools等效？）检查是否安装了直接依赖项，但不是安装了那些依赖项等。可能发生的事情是您设法安装了一个依赖项，但是通过删除其中一个依赖项（通过remove.packages()手动删除，或更改.libPaths()或者......）来破坏您的安装很高兴听到你对这可能发生的任何猜测。）

一种解决方案是找到所有可用的包

avail = available.packages(repos=BiocInstaller::biocinstallRepos())

然后是所有依赖项

deps0 = tools::package_depenencies("DESeq2", avail)
deps = unique(unlist(deps0, use.names=FALSE))

和不满意的依赖

need = setdiff(deps, rownames(installed.packages()))

我要查看need，看看是否有任何见解，以便您可以纠正根本问题，而不必与其他软件包一起执行此过程。最后，安装问题包，也许还有DESeq2。

biocLite(c(need, "DESeq2"))

在Bioconductor领域，我会检查包装版本是否与使用中的Bioconductor版本一致

BiocInstaller::biocValid()

并会在Bioconductor上提出更多与Bioconductor相关的问题support site

答案 2 :(得分：1)

这是我在Hack-R评论中写的相同答案我只是想发表一个单独的答案：

我所做的是 - 卸载所有内容（RTools然后是RStudio thenR，我也删除了R目录，因为它仍然拥有所有以前的库）我这样做是为了消除任何可能存在腐败的可能性。

（我突出显示重点）：

然后我重新安装R然后Rstudio然后重新安装RTools。我再次尝试使用biocLite进行安装，但是遇到了缺少软件包的错误（或者安装没问题，当我尝试加载DESeq2库时遇到了丢失的软件包错误）所以 I改变了RStudio中的CRAN镜像。我再次尝试使用biocLite进行安装，并再次遇到丢失的软件包（或者安装正常，当我尝试加载DESeq2库时遇到了丢失的软件包错误，我不记得了）但是！ ！现在，当我尝试手动安装丢失的软件包时（使用install.packages（＆＃34; missingPackage＆＃34;））它们确实正确安装。最后在3-4次手动安装后丢失包装一切都有效。

抱歉平庸的英语。

我希望我帮助过某个人。

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