R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> options("repos" = c(CRAN="http://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
> if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
載入需要的程輯包：BiocManager
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
>
> options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
>
> cran_packages <- c('tidyr',
+ 'tibble',
+ 'dplyr',
+ 'stringr',
+ 'ggplot2',
+ 'ggpubr',
+ 'factoextra',
+ 'FactoMineR',
+ 'pheatmap',
+ "survival",
+ "survminer",
+ "patchwork",
+ "ggstatsplot",
+ "ggplotify",
+ "cowplot",
+ "glmnet",
+ "ROCR",
+ "caret",
+ "randomForest",
+ "survminer",
+ "Hmisc",
+ "e1071",
+ "deconstructSigs",
+ "timeROC"
+ )
> Biocductor_packages <- c("KEGG.db",
+ "limma",
+ "clusterProfiler",
+ "org.Hs.eg.db",
+ "SummarizedExperiment",
+ "DESeq2",
+ "edgeR",
+ "ggpubr",
+ "rtracklayer",
+ "genefilter",
+ "maftools",
+ "ComplexHeatmap",
+ "GDCRNATools"
+ )
>
>
> for (pkg in cran_packages){
+ if (! require(pkg,character.only=T) ) {
+ install.packages(pkg,ask = F,update = F)
+ require(pkg,character.only=T)
+ }
+ }
載入需要的程輯包：tidyr
載入需要的程輯包：tibble
載入需要的程輯包：dplyr
載入程輯包：‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
載入需要的程輯包：stringr
載入需要的程輯包：ggplot2
Use suppressPackageStartupMessages() to eliminate package startup messages
載入需要的程輯包：ggpubr
載入需要的程輯包：factoextra
Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
載入需要的程輯包：FactoMineR
載入需要的程輯包：pheatmap
載入需要的程輯包：survival
載入需要的程輯包：survminer
載入需要的程輯包：patchwork
載入需要的程輯包：ggstatsplot
Registered S3 methods overwritten by 'lme4':
method from
cooks.distance.influence.merMod car
influence.merMod car
dfbeta.influence.merMod car
dfbetas.influence.merMod car
In case you would like cite this package, cite it as:
Patil, I. (2018). ggstatsplot: "ggplot2" Based Plots with Statistical Details. CRAN.
Retrieved from https://cran.r-project.org/web/packages/ggstatsplot/index.html
載入需要的程輯包：ggplotify
載入需要的程輯包：cowplot
載入程輯包：‘cowplot’
The following object is masked from ‘package:patchwork’:
align_plots
The following object is masked from ‘package:ggpubr’:
get_legend
載入需要的程輯包：glmnet
載入需要的程輯包：Matrix
載入程輯包：‘Matrix’
The following objects are masked from ‘package:tidyr’:
expand, pack, unpack
Loaded glmnet 4.1
載入需要的程輯包：ROCR
載入需要的程輯包：caret
載入需要的程輯包：lattice
載入程輯包：‘caret’
The following object is masked from ‘package:survival’:
cluster
載入需要的程輯包：randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
載入程輯包：‘randomForest’
The following object is masked from ‘package:ggplot2’:
margin
The following object is masked from ‘package:dplyr’:
combine
載入需要的程輯包：Hmisc
載入需要的程輯包：Formula
載入程輯包：‘Hmisc’
The following objects are masked from ‘package:dplyr’:
src, summarize
The following objects are masked from ‘package:base’:
format.pval, units
載入需要的程輯包：e1071
載入程輯包：‘e1071’
The following object is masked from ‘package:Hmisc’:
impute
載入需要的程輯包：deconstructSigs
載入需要的程輯包：timeROC
>
>
> # use BiocManager to install
> for (pkg in Biocductor_packages){
+ if (! require(pkg,character.only=T) ) {
+ BiocManager::install(pkg,ask = F,update = F)
+ require(pkg,character.only=T)
+ }
+ }
載入需要的程輯包：KEGG.db
載入需要的程輯包：AnnotationDbi
載入需要的程輯包：stats4
載入需要的程輯包：BiocGenerics
載入需要的程輯包：parallel
載入程輯包：‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
parSapplyLB
The following object is masked from ‘package:randomForest’:
combine
The following objects are masked from ‘package:dplyr’:
combine, intersect, setdiff, union
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, 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, which.max, which.min
載入需要的程輯包：Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.
載入程輯包：‘Biobase’
The following object is masked from ‘package:Hmisc’:
contents
載入需要的程輯包：IRanges
載入需要的程輯包：S4Vectors
載入程輯包：‘S4Vectors’
The following object is masked from ‘package:Matrix’:
expand
The following objects are masked from ‘package:dplyr’:
first, rename
The following object is masked from ‘package:tidyr’:
expand
The following object is masked from ‘package:base’:
expand.grid
載入程輯包：‘IRanges’
The following objects are masked from ‘package:dplyr’:
collapse, desc, slice
The following object is masked from ‘package:grDevices’:
windows
載入程輯包：‘AnnotationDbi’
The following object is masked from ‘package:dplyr’:
select
KEGG.db contains mappings based on older data because the original resource was
removed from the the public domain before the most recent update was produced.
This package should now be considered deprecated and future versions of
Bioconductor may not have it available. Users who want more current data are
encouraged to look at the KEGGREST or reactome.db packages
載入需要的程輯包：limma
載入程輯包：‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
載入需要的程輯包：clusterProfiler
clusterProfiler v3.18.0 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
載入程輯包：‘clusterProfiler’
The following object is masked from ‘package:AnnotationDbi’:
select
The following object is masked from ‘package:IRanges’:
slice
The following object is masked from ‘package:S4Vectors’:
rename
The following object is masked from ‘package:lattice’:
dotplot
The following object is masked from ‘package:stats’:
filter
載入需要的程輯包：org.Hs.eg.db
載入需要的程輯包：SummarizedExperiment
載入需要的程輯包：MatrixGenerics
載入需要的程輯包：matrixStats
載入程輯包：‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
The following object is masked from ‘package:dplyr’:
count
載入程輯包：‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts,
colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs,
colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians,
colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks,
colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars,
colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2,
rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges,
rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds,
rowWeightedVars
The following object is masked from ‘package:Biobase’:
rowMedians
載入需要的程輯包：GenomicRanges
載入需要的程輯包：GenomeInfoDb
載入需要的程輯包：DESeq2
載入需要的程輯包：edgeR
載入需要的程輯包：rtracklayer
載入需要的程輯包：genefilter
載入程輯包：‘genefilter’
The following objects are masked from ‘package:MatrixGenerics’:
rowSds, rowVars
The following objects are masked from ‘package:matrixStats’:
rowSds, rowVars
The following object is masked from ‘package:patchwork’:
area
載入需要的程輯包：maftools
載入程輯包：‘maftools’
The following object is masked from ‘package:deconstructSigs’:
plotSignatures
載入需要的程輯包：ComplexHeatmap
載入需要的程輯包：grid
========================================
ComplexHeatmap version 2.6.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
! pheatmap() has been masked by ComplexHeatmap::pheatmap(). 90% of the arguments
in the original pheatmap() are identically supported in the new function. You
can still use the original function by explicitly calling pheatmap::pheatmap().
載入程輯包：‘ComplexHeatmap’
The following object is masked from ‘package:genefilter’:
dist2
The following object is masked from ‘package:pheatmap’:
pheatmap
載入需要的程輯包：GDCRNATools
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Registered S3 method overwritten by 'gplots':
method from
reorder.factor DescTools
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor version 3.12
>
>
> #前面的報錯都先不要管。主要看這里
> for (pkg in c(Biocductor_packages,cran_packages)){
+ require(pkg,character.only=T)
+ }
>
> #哪個報錯类少，就回去安裝哪個很泊。如果你沒有安裝xx包贝次，卻提示你xx包不存在昭娩，這也正常，是因為復(fù)雜的依賴關(guān)系宪郊，缺啥補啥艰匙。
> if(!require(AnnoProbe))devtools::install_local("AnnoProbe-master.zip",upgrade = F,dependencies = T)
載入需要的程輯包：AnnoProbe
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
AnnoProbe v 0.1.0 welcome to use AnnoProbe!
If you use AnnoProbe in published research, please acknowledgements:
We thank Dr.Jianming Zeng(University of Macau), and all the members of his bioinformatics team, biotrainee, for generously sharing their experience and codes.
> if(!require(tinyarray))devtools::install_local("tinyarray-master.zip",upgrade = F,dependencies = T)
載入需要的程輯包：tinyarray
載入程輯包：‘tinyarray’
The following object is masked from ‘package:dplyr’:
union_all
> library(AnnoProbe)
> library(tinyarray)
