2020-04-08seurat版本降级安装过程

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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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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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:/PROGRA_1/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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2020-04-08seurat版本降级安装过程

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install.packages("Seurat") #先装个3.0版本

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