- html - 出于某种原因,IE8 对我的 Sass 文件中继承的 html5 CSS 不友好?
- JMeter 在响应断言中使用 span 标签的问题
- html - 在 :hover and :active? 上具有不同效果的 CSS 动画
- html - 相对于居中的 html 内容固定的 CSS 重复背景?
我在安装和使用 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")
但它遇到了很多错误(某些依赖包缺少一些包等...)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,我希望它们的信息将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 DESeq2 软件包时一切都很顺利......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’
尝试安装缺少的软件包:
> 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 session 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 个软件包,所以我认为解决方案不是继续安装丢失的软件包,因为这些软件包将有更多丢失的软件包,而且越来越多,我将无法摆脱这个循环。
我还尝试了在谷歌上找到的东西:
remove.packages(c("ggplot2", "data.table"))
install.packages('Rcpp', dependencies = TRUE)
install.packages('ggplot2', dependencies = TRUE)
但是安装也有错误,如果需要的话我可以把它们写在这里。
我希望您能看到我看不到的东西并帮助我解决这个问题。
谢谢。
最佳答案
看起来包很多,最重要的是data.table
和lme4
,未正确编译。
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:
的 2 条语句中表示的所有软件包与 pacman
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")
我刚刚确认这可以在 Windows 上运行。
但请注意,您收到的错误 has been associated过去有镜像中断。 因此,如果您仍然收到此错误,请尝试更改您的 CRAN 镜像。 install.packages('<package_name>', repo='http://nbcgib.uesc.br/mirrors/cran/')
还要确保您已安装并运行 RTools.exe。
关于r - 无法加载 R DESeq2 库,安装了所有缺失的软件包,但仍然存在问题,我们在Stack Overflow上找到一个类似的问题: https://stackoverflow.com/questions/39447207/
每次我尝试构建(执行完整的 Clean,然后构建)时,我都会在 Eclipse 的问题部分下弹出此错误消息。项目本身旁边还显示一个错误。 我已经尝试了同一问题的其他解决方案中包含的所有内容: 删除项目
我收到以下错误(注意:我使用的是 Netbeans): java.sql.SQLException: No suitable driver found for jdbc:derby://localho
例如 //somewhere struct IFace; struct Base { Base(IFace* iface): f(iface) { //wi
我试图通过 stringstream 将 double 变成字符串,但它不起作用。 std::string MatlabPlotter::getTimeVector( unsigned int xve
我正在尝试使用 AudioKit 框架中的音序器播放音频文件。 AudioKit.output = sampler AudioKit.start() sampler.enableMID
昨天我问了一个关于插入 Heroku 的问题。它不工作,然后突然开始工作。我什么都没改变。现在在一个新的应用程序上,我遇到了完全相同的问题。我决定包含我的整个 Gemfile,希望我可以继续没有这种令
我知道,这个topic已经是discussed许多times,所以直截了当。 这是ItemsSource的TabControl: Tabs = new ObservableCollection {
我有一个更新对象的函数,问题是当我从更新表单字段返回到详细 View 时,它初始化旧对象而不是更新后的对象。 我想在 CarService 而不是 app.js 中填充汽车列表 这是我的汽车服务:
在 resolution comments错误报告 12266 (“套接字连接错误导致资源泄漏”),Robert Ehteshamzadeh 写道 TClientSocket is deprecate
我最初发布了一个问题 here 我发现 JTextField 仅在 JScrollPane 存在时才调整大小。换句话说,我可以根据需要最小化和最大化它,直到出现滚动条(因为文本太多,无法放入窗口)。之
我读过关于 postion:absolute 的问题并尝试了几乎所有可能的解决方案。包括相对定位 div,将它们包装在相对定位的父级中等等,但它没有帮助。 我正在绘制一个表格,然后我将 div 放入其
我在这里发起了一个话题document.getElementById not working但看起来即使提出的建议都是有效的,我仍然有问题。 我有几个复选框。当我在这里查看页面源代码时,有。 docu
我正在做一些阅读,试图更好地理解按位运算符,然后偶然发现了 a helpful old blog post from 2012 ,其中指出 - 在随机正整数 x 的奇数测试中 - 在作者的计算机上评估
我正在尝试在 Eclipse Neon 中使用 aspectj 创建一个示例 maven 项目。然而,方面并没有编织/工作(参见下面的输出)。我尝试寻找很多原因和解决方案,但没有一个有效(请参阅下面的
无论我如何配置我的 appsettings.json 和 appsettings.Development.json,除非我手动添加 ConfigureLogging,否则我无法在信息消息下方记录任何内
我正在尝试使用 JQuery .get() 方法和 JavaScript for 循环来处理来自外部文件的一些数据。我已经在 stackoverflow 上阅读了有关闭包和回调返回值的内容几个小时,但
我正在使用 PHP 5.6 并且要打印一些东西,我必须编辑 php.ini 并包含 php_printer.dll 文件。但是 PHP 5.6 没有.dll 文件。 我要解决的问题: 我想将凭证打印机
我目前正在调试一个包含内存泄漏的大(非常大!)C# 应用程序。它主要使用 Winforms 作为 GUI,尽管一些控件是在 WPF 中制作的,并由 ElementHost 托管。直到现在,我发现许多内
[已解决] 看来 PHP MYADMIN 变量成功了。我将 wait_timeout 设置为 30 ,并将 Lock_wait_timeout 设置为 50 花了将近 6 个小时才恢复稳定,包括几次重
我读过几个关于该主题的讨论,有人说 qmake < 3.0 不正确支持该指令。我刚刚为 g++-64 重新安装了 Qt 5.9.1,但问题仍然存在。此外,我尝试过各种 mkspecs/xxx/xxx.
我是一名优秀的程序员,十分优秀!