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2020-04-08seurat版本降级安装过程

2020-04-08seurat版本降级安装过程

作者: Seurat_Satija | 来源:发表于2020-04-08 10:58 被阅读0次

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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3.1.1 降为2.3.4
library(Seurat)
Error in library(Seurat) : 不存在叫‘Seurat’这个名字的程辑包

---------------

install.packages("Seurat") #先装个3.0版本

library(Seurat)
Error in library(Seurat) : 不存在叫‘Seurat’这个名字的程辑包
packageurl <- "https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
Installing package into ‘C:/Users/wlx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz'
Content type 'application/x-gzip' length 861959 bytes (841 KB)
downloaded 841 KB

  • installing source package 'Seurat' ...
    ** 成功将'Seurat'程序包解包并MD5和检查
    ** using staged installation
    ** libs
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c ModularityOptimizer.cpp -o ModularityOptimizer.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c RModularityOptimizer.cpp -o RModularityOptimizer.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c data_manipulation.cpp -o data_manipulation.o
    data_manipulation.cpp: In function 'Eigen::SparseMatrix<double, 0, int> RowMergeMatrices(Eigen::SparseMatrix<double, 1, int>, Eigen::SparseMatrix<double, 1, int>, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >)':
    data_manipulation.cpp:79:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int i = 0; i < mat1_rownames.size(); i++){
    ^
    data_manipulation.cpp:83:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int i = 0; i < mat2_rownames.size(); i++){
    ^
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c snn.cpp -o snn.o
    C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Seurat.dll tmp.def ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o snn.o -LC:/PROGRA1/R/R-361.2/bin/x64 -lR
    installing to C:/Users/wlx/Documents/R/win-library/3.6/00LOCK-Seurat/00new/Seurat/libs/x64
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
    there is no package called 'knitr'
    Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    停止执行
    ERROR: lazy loading failed for package 'Seurat'
  • removing 'C:/Users/wlx/Documents/R/win-library/3.6/Seurat'
    Warning in install.packages :
    installation of package ‘C:/WINDOWS/Temp/RtmpUtXKlM/downloaded_packages/Seurat_2.3.4.tar.gz’ had non-zero exit status
    library(Seurat)
    Error in library(Seurat) : 不存在叫‘Seurat’这个名字的程辑包

install.packages("knitr")
Installing package into ‘C:/Users/wlx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘evaluate’, ‘highr’, ‘markdown’, ‘xfun’

trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/evaluate_0.14.zip'
Content type 'application/zip' length 76868 bytes (75 KB)
downloaded 75 KB

trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/highr_0.8.zip'
Content type 'application/zip' length 48714 bytes (47 KB)
downloaded 47 KB

trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/markdown_1.1.zip'
Content type 'application/zip' length 190190 bytes (185 KB)
downloaded 185 KB

trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/xfun_0.12.zip'
Content type 'application/zip' length 183537 bytes (179 KB)
downloaded 179 KB

trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/knitr_1.28.zip'
Content type 'application/zip' length 1428929 bytes (1.4 MB)
downloaded 1.4 MB

package ‘evaluate’ successfully unpacked and MD5 sums checked
package ‘highr’ successfully unpacked and MD5 sums checked
package ‘markdown’ successfully unpacked and MD5 sums checked
package ‘xfun’ successfully unpacked and MD5 sums checked
package ‘knitr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Windows\Temp\RtmpUtXKlM\downloaded_packages

library(Seurat)
Error in library(Seurat) : 不存在叫‘Seurat’这个名字的程辑包
packageurl <- "https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
Installing package into ‘C:/Users/wlx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz'
Content type 'application/x-gzip' length 861959 bytes (841 KB)
downloaded 841 KB

  • installing source package 'Seurat' ...
    ** 成功将'Seurat'程序包解包并MD5和检查
    ** using staged installation
    ** libs
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c ModularityOptimizer.cpp -o ModularityOptimizer.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c RModularityOptimizer.cpp -o RModularityOptimizer.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c data_manipulation.cpp -o data_manipulation.o
    data_manipulation.cpp: In function 'Eigen::SparseMatrix<double, 0, int> RowMergeMatrices(Eigen::SparseMatrix<double, 1, int>, Eigen::SparseMatrix<double, 1, int>, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >)':
    data_manipulation.cpp:79:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int i = 0; i < mat1_rownames.size(); i++){
    ^
    data_manipulation.cpp:83:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int i = 0; i < mat2_rownames.size(); i++){
    ^
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c snn.cpp -o snn.o
    C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Seurat.dll tmp.def ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o snn.o -LC:/PROGRA1/R/R-361.2/bin/x64 -lR
    installing to C:/Users/wlx/Documents/R/win-library/3.6/00LOCK-Seurat/00new/Seurat/libs/x64
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
    there is no package called 'rstudioapi'
    Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    停止执行
    ERROR: lazy loading failed for package 'Seurat'
  • removing 'C:/Users/wlx/Documents/R/win-library/3.6/Seurat'
    Warning in install.packages :
    installation of package ‘C:/WINDOWS/Temp/RtmpUtXKlM/downloaded_packages/Seurat_2.3.4.tar.gz’ had non-zero exit status

install.packages('rstudioapi')
Installing package into ‘C:/Users/wlx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/rstudioapi_0.11.zip'
Content type 'application/zip' length 281270 bytes (274 KB)
downloaded 274 KB

package ‘rstudioapi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Windows\Temp\RtmpUtXKlM\downloaded_packages

library(Seurat)
Error in library(Seurat) : 不存在叫‘Seurat’这个名字的程辑包
install.packages(packageurl, repos=NULL, type="source")
Installing package into ‘C:/Users/wlx/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_2.3.4.tar.gz'
Content type 'application/x-gzip' length 861959 bytes (841 KB)
downloaded 841 KB

  • installing source package 'Seurat' ...
    ** 成功将'Seurat'程序包解包并MD5和检查
    ** using staged installation
    ** libs
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c ModularityOptimizer.cpp -o ModularityOptimizer.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c RModularityOptimizer.cpp -o RModularityOptimizer.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c data_manipulation.cpp -o data_manipulation.o
    data_manipulation.cpp: In function 'Eigen::SparseMatrix<double, 0, int> RowMergeMatrices(Eigen::SparseMatrix<double, 1, int>, Eigen::SparseMatrix<double, 1, int>, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<std::basic_string<char> >)':
    data_manipulation.cpp:79:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int i = 0; i < mat1_rownames.size(); i++){
    ^
    data_manipulation.cpp:83:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int i = 0; i < mat2_rownames.size(); i++){
    ^
    C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.2/include" -DNDEBUG -I"C:/Users/wlx/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/wlx/Documents/R/win-library/3.6/RcppProgress/include" -O2 -Wall -mtune=generic -c snn.cpp -o snn.o
    C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Seurat.dll tmp.def ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o snn.o -LC:/PROGRA1/R/R-361.2/bin/x64 -lR
    installing to C:/Users/wlx/Documents/R/win-library/3.6/00LOCK-Seurat/00new/Seurat/libs/x64
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    converting help for package 'Seurat'
    finding HTML links ... 好了
    AddImputedScore html
    AddMetaData html
    AddModuleScore html
    AddSamples html
    AddSmoothedScore html
    AlignSubspace html
    AssessNodes html
    AssessSplit html
    AugmentPlot html
    AverageDetectionRate html
    AverageExpression html
    AveragePCA html
    BatchGene html
    BlackAndWhite html
    BuildClusterTree html
    BuildRFClassifier html
    BuildSNN html
    CalcAlignmentMetric html
    CalcVarExpRatio html
    CaseMatch html
    CellCycleScoring html
    CellPlot html
    ClassifyCells html
    CollapseSpeciesExpressionMatrix html
    ColorTSNESplit html
    CombineIdent html
    Convert html
    CreateSeuratObject html
    CustomDistance html
    CustomPalette html
    DBClustDimension html
    DESeq2DETest html
    DMEmbed html
    DMPlot html
    DarkTheme html
    DiffExpTest html
    DiffTTest html
    DimElbowPlot html
    DimHeatmap html
    DimPlot html
    DimTopCells html
    DimTopGenes html
    DoHeatmap html
    DoKMeans html
    DotPlot html
    DotPlotOld html
    ExpMean html
    ExpSD html
    ExpVar html
    ExtractField html
    FastWhichCells html
    FeatureHeatmap html
    FeatureLocator html
    FeaturePlot html
    FetchData html
    FilterCells html
    FindAllMarkers html
    FindAllMarkersNode html
    FindClusters html
    FindConservedMarkers html
    FindGeneTerms html
    FindMarkers html
    FindMarkersNode html
    FindVariableGenes html
    FitGeneK html
    GenePlot html
    GenesInCluster html
    GetAssayData html
    GetCellEmbeddings html
    GetCentroids html
    GetClusters html
    GetDimReduction html
    GetGeneLoadings html
    GetIdent html
    HTODemux html
    HTOHeatmap html
    HoverLocator html
    ICAEmbed html
    ICALoad html
    ICAPlot html
    ICHeatmap html
    ICTopCells html
    ICTopGenes html
    InitialMapping html
    JackStraw html
    JackStrawPlot html
    KClustDimension html
    KMeansHeatmap html
    LogNormalize html
    LogVMR html
    MASTDETest html
    MakeSparse html
    MarkerTest html
    MatrixRowShuffle html
    MergeNode html
    MergeSeurat html
    MetageneBicorPlot html
    MinMax html
    MultiModal_CCA html
    MultiModal_CIA html
    NegBinomDETest html
    NegBinomRegDETest html
    NormalizeData html
    NumberClusters html
    OldDoHeatmap html
    PCAEmbed html
    PCALoad html
    PCAPlot html
    PCASigGenes html
    PCElbowPlot html
    PCHeatmap html
    PCTopCells html
    PCTopGenes html
    PlotClusterTree html
    PoissonDETest html
    PrintAlignSubspaceParams html
    PrintCCAParams html
    PrintCalcParams html
    PrintCalcVarExpRatioParams html
    PrintDMParams html
    PrintDim html
    PrintFindClustersParams html
    PrintICA html
    PrintICAParams html
    PrintPCA html
    PrintPCAParams html
    PrintSNNParams html
    PrintTSNEParams html
    ProjectDim html
    ProjectPCA html
    PurpleAndYellow html
    Read10X html
    Read10X_h5 html
    RefinedMapping html
    RemoveFromTable html
    RenameCells html
    RenameIdent html
    ReorderIdent html
    RidgePlot html
    RunCCA html
    RunDiffusion html
    RunICA html
    RunMultiCCA html
    RunPCA html
    RunPHATE html
    RunTSNE html
    RunUMAP html
    SampleUMI html
    SaveClusters html
    ScaleData html
    ScaleDataR html
    SetAllIdent html
    SetAssayData html
    SetClusters html
    SetDimReduction html
    SetIdent html
    Seurat-deprecated html
    Shuffle html
    SplitDotPlotGG html
    SplitObject html
    StashIdent html
    SubsetByPredicate html
    SubsetColumn html
    SubsetData html
    SubsetRow html
    TSNEPlot html
    TobitTest html
    TransferIdent html
    UpdateSeuratObject html
    ValidateClusters html
    ValidateSpecificClusters html
    VariableGenePlot html
    VizDimReduction html
    VizICA html
    VizPCA html
    VlnPlot html
    WhichCells html
    WilcoxDETest html
    cc.genes html
    pbmc_small html
    seurat html
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (Seurat)

library(Seurat)
载入需要的程辑包：ggplot2
载入需要的程辑包：cowplot

Note: As of version 1.0.0, cowplot does not change the
default ggplot2 theme anymore. To recover the previous
behavior, execute:
theme_set(theme_cowplot())

载入需要的程辑包：Matrix

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