无法加载 R DESeq2 库，已安装所有缺少的包，但仍有问题
Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems
我运行在安装和使用 R 的 DESeq2 包时遇到了一些严重问题。
我在 Win7 上新安装了 R 3.3.1 和 Rstudio 0.99.903。
我尝试使用以下方法安装 DESeq2：
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
但它 运行 出现了很多错误（一些依赖包缺少包等...）然后我尝试通过从 CREN 下载并从 .压缩文件。
然后我尝试了 运行ning 几个命令，我希望它们提供的信息能帮助找到所有错误的原因：
首先是 biocLite（所有相关包的安装程序，在之前安装 DESeq2 包时一切都很顺利...但它在 Linux）
> 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 包（看起来一切正常）
> 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
正在加载 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’
尝试安装丢失的包：
> 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’
和会话信息：
> 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 10 个以上的包，所以我认为解决方案不是继续安装丢失的包，因为这些包将有更多丢失的包，而且越来越多，我将无法摆脱这个循环。
我还尝试了在 google 上找到的东西：
remove.packages(c("ggplot2", "data.table"))
install.packages('Rcpp', dependencies = TRUE)
install.packages('ggplot2', dependencies = TRUE)
但是安装也有错误，需要的话可以写在这里
希望你能看到我看不到的东西，帮我解决这个问题。
谢谢。
似乎很多包，最重要的是 data.table 和 lme4，都没有正确编译。
我建议安装 data.table、lme4 以及在 Packages which are only available in source form, and may need compilation of C/C++/Fortran: 和 pacman 的 2 个语句中表示的所有软件包，然后重新 运行 目标包的 Bioconductor 安装。
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。
然而，另请注意，您在过去 has been associated 由于镜像中断而遇到的错误。 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/')
还要确保您已 RTools.exe 安装并正常工作。
biocLite()、install.packages()（以及等效的 devtools？）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，但随后通过删除其中一个依赖项（手动通过 remove.packages()，或更改 .libPaths()，或者...来破坏您的安装？这将是一件好事听听您对这可能是如何发生的任何猜测）。
一个解决方案是找到所有可用的包
avail = available.packages(repos=BiocInstaller::biocinstallRepos())
然后所有依赖项
deps0 = tools::package_depenencies("DESeq2", avail)
deps = unique(unlist(deps0, use.names=FALSE))
和不满足的依赖关系
need = setdiff(deps, rownames(installed.packages()))
我会看一下 need，看看是否有任何见解，以便您可以更正根本问题，而不必对其他软件包执行此过程。最后，安装问题包，也许还有 DESeq2。
biocLite(c(need, "DESeq2"))
在 Bioconductor 领域，我会检查包版本是否与正在使用的 Bioconductor 版本一致
BiocInstaller::biocValid()
并且会在 Bioconductor 上提出更多与 Bioconductor 相关的问题 support site
这与我在对 Hack-R 的评论中写的相同答案我只是想 post 一个单独的答案：
我所做的是 - 卸载了所有东西（RTools，然后是 RStudio，然后是 R，我还删除了 R 目录，因为它仍然有所有以前的库）我这样做是为了消除任何损坏的可能性。
（我强调要点）：
然后我重新安装了 R，然后是 Rstudio，然后是 RTools。我再次尝试使用 biocLite 安装，但是 遇到了缺少包的错误 （或者安装没问题，当我尝试加载 DESeq2 库时遇到了缺少包的错误）所以 我在RStudio中更改了CRAN镜像。我再次尝试使用 biocLite 进行安装，但又遇到了丢失的包（或者安装正常，当我尝试加载 DESeq2 库时遇到了丢失包的错误，我不记得了）但是！ ！！现在，当我尝试手动安装缺少的软件包时（使用install.packages（"missingPackage"））它们确实安装正确。 最后在 3-4 手册之后安装丢失的软件包一切正常。
抱歉，英语水平一般。
我希望我帮助了别人。
我运行在安装和使用 R 的 DESeq2 包时遇到了一些严重问题。
我在 Win7 上新安装了 R 3.3.1 和 Rstudio 0.99.903。 我尝试使用以下方法安装 DESeq2：
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
但它 运行 出现了很多错误（一些依赖包缺少包等...）然后我尝试通过从 CREN 下载并从 .压缩文件。
然后我尝试了 运行ning 几个命令，我希望它们提供的信息能帮助找到所有错误的原因： 首先是 biocLite（所有相关包的安装程序，在之前安装 DESeq2 包时一切都很顺利...但它在 Linux）
> 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 包（看起来一切正常）
> 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
正在加载 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’
尝试安装丢失的包：
> 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’
和会话信息：
> 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 10 个以上的包，所以我认为解决方案不是继续安装丢失的包，因为这些包将有更多丢失的包，而且越来越多，我将无法摆脱这个循环。
我还尝试了在 google 上找到的东西：
remove.packages(c("ggplot2", "data.table"))
install.packages('Rcpp', dependencies = TRUE)
install.packages('ggplot2', dependencies = TRUE)
但是安装也有错误，需要的话可以写在这里
希望你能看到我看不到的东西，帮我解决这个问题。
谢谢。
似乎很多包，最重要的是 data.table 和 lme4，都没有正确编译。
我建议安装 data.table、lme4 以及在 Packages which are only available in source form, and may need compilation of C/C++/Fortran: 和 pacman 的 2 个语句中表示的所有软件包，然后重新 运行 目标包的 Bioconductor 安装。
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。
然而，另请注意，您在过去 has been associated 由于镜像中断而遇到的错误。 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/')
还要确保您已 RTools.exe 安装并正常工作。
biocLite()、install.packages()（以及等效的 devtools？）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，但随后通过删除其中一个依赖项（手动通过 remove.packages()，或更改 .libPaths()，或者...来破坏您的安装？这将是一件好事听听您对这可能是如何发生的任何猜测）。
一个解决方案是找到所有可用的包
avail = available.packages(repos=BiocInstaller::biocinstallRepos())
然后所有依赖项
deps0 = tools::package_depenencies("DESeq2", avail)
deps = unique(unlist(deps0, use.names=FALSE))
和不满足的依赖关系
need = setdiff(deps, rownames(installed.packages()))
我会看一下 need，看看是否有任何见解，以便您可以更正根本问题，而不必对其他软件包执行此过程。最后，安装问题包，也许还有 DESeq2。
biocLite(c(need, "DESeq2"))
在 Bioconductor 领域，我会检查包版本是否与正在使用的 Bioconductor 版本一致
BiocInstaller::biocValid()
并且会在 Bioconductor 上提出更多与 Bioconductor 相关的问题 support site
这与我在对 Hack-R 的评论中写的相同答案我只是想 post 一个单独的答案：
我所做的是 - 卸载了所有东西（RTools，然后是 RStudio，然后是 R，我还删除了 R 目录，因为它仍然有所有以前的库）我这样做是为了消除任何损坏的可能性。
（我强调要点）：
然后我重新安装了 R，然后是 Rstudio，然后是 RTools。我再次尝试使用 biocLite 安装，但是 遇到了缺少包的错误 （或者安装没问题，当我尝试加载 DESeq2 库时遇到了缺少包的错误）所以 我在RStudio中更改了CRAN镜像。我再次尝试使用 biocLite 进行安装，但又遇到了丢失的包（或者安装正常，当我尝试加载 DESeq2 库时遇到了丢失包的错误，我不记得了）但是！ ！！现在，当我尝试手动安装缺少的软件包时（使用install.packages（"missingPackage"））它们确实安装正确。 最后在 3-4 手册之后安装丢失的软件包一切正常。
抱歉，英语水平一般。
我希望我帮助了别人。