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
help(package="Seurat")
packageVersion("Seurat")
[1] ‘2.3.4’
BiocManager::install('monocle')
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'monocle'
also installing the dependencies ‘sparsesvd’, ‘docopt’, ‘graph’, ‘RBGL’, ‘XML’, ‘RCurl’, ‘RUnit’, ‘VGAM’, ‘DDRTree’, ‘HSMMSingleCell’, ‘combinat’, ‘fastICA’, ‘matrixStats’, ‘densityClust’, ‘limma’, ‘qlcMatrix’, ‘pheatmap’, ‘slam’, ‘viridis’, ‘biocViews’
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/sparsesvd_0.2.zip'
Content type 'application/zip' length 72474 bytes (70 KB)
downloaded 70 KB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/docopt_0.6.1.zip'
Content type 'application/zip' length 181486 bytes (177 KB)
downloaded 177 KB
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/graph_1.64.0.zip'
Content type 'application/zip' length 1765572 bytes (1.7 MB)
downloaded 1.7 MB
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/RBGL_1.62.1.zip'
Content type 'application/zip' length 3558191 bytes (3.4 MB)
downloaded 3.4 MB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/XML_3.99-0.3.zip'
Content type 'application/zip' length 4258943 bytes (4.1 MB)
downloaded 4.1 MB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/RCurl_1.98-1.1.zip'
Content type 'application/zip' length 2988412 bytes (2.8 MB)
downloaded 2.8 MB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/RUnit_0.4.32.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/RUnit_0.4.32.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
InternetOpenUrl failed: '操作超时'
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘RUnit’ failed
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/VGAM_1.1-2.zip'
Content type 'application/zip' length 8352001 bytes (8.0 MB)
downloaded 8.0 MB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/DDRTree_0.1.5.zip'
Content type 'application/zip' length 754856 bytes (737 KB)
downloaded 737 KB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/combinat_0.0-8.zip'
Content type 'application/zip' length 43075 bytes (42 KB)
downloaded 42 KB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/fastICA_1.2-2.zip'
Content type 'application/zip' length 62101 bytes (60 KB)
downloaded 60 KB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/matrixStats_0.56.0.zip'
Content type 'application/zip' length 1727933 bytes (1.6 MB)
downloaded 1.6 MB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/densityClust_0.3.zip'
Content type 'application/zip' length 600592 bytes (586 KB)
downloaded 586 KB
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/limma_3.42.2.zip'
Content type 'application/zip' length 3096814 bytes (3.0 MB)
downloaded 3.0 MB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/qlcMatrix_0.9.7.zip'
Content type 'application/zip' length 3299422 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/pheatmap_1.0.12.zip'
Content type 'application/zip' length 78715 bytes (76 KB)
downloaded 76 KB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/slam_0.1-47.zip'
Content type 'application/zip' length 211121 bytes (206 KB)
downloaded 206 KB
trying URL 'https://mirrors.ustc.edu.cn/CRAN/bin/windows/contrib/3.6/viridis_0.5.1.zip'
Content type 'application/zip' length 1866771 bytes (1.8 MB)
downloaded 1.8 MB
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/biocViews_1.54.0.zip'
Content type 'application/zip' length 633907 bytes (619 KB)
downloaded 619 KB
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/monocle_2.14.0.zip'
Content type 'application/zip' length 1955525 bytes (1.9 MB)
downloaded 1.9 MB
package ‘sparsesvd’ successfully unpacked and MD5 sums checked
package ‘docopt’ successfully unpacked and MD5 sums checked
package ‘graph’ successfully unpacked and MD5 sums checked
package ‘RBGL’ successfully unpacked and MD5 sums checked
package ‘XML’ successfully unpacked and MD5 sums checked
package ‘RCurl’ successfully unpacked and MD5 sums checked
package ‘VGAM’ successfully unpacked and MD5 sums checked
package ‘DDRTree’ successfully unpacked and MD5 sums checked
package ‘combinat’ successfully unpacked and MD5 sums checked
package ‘fastICA’ successfully unpacked and MD5 sums checked
package ‘matrixStats’ successfully unpacked and MD5 sums checked
package ‘densityClust’ successfully unpacked and MD5 sums checked
package ‘limma’ successfully unpacked and MD5 sums checked
package ‘qlcMatrix’ successfully unpacked and MD5 sums checked
package ‘pheatmap’ successfully unpacked and MD5 sums checked
package ‘slam’ successfully unpacked and MD5 sums checked
package ‘viridis’ successfully unpacked and MD5 sums checked
package ‘biocViews’ successfully unpacked and MD5 sums checked
package ‘monocle’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Windows\Temp\RtmpwfgZbY\downloaded_packages
installing the source package ‘HSMMSingleCell’
trying URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/HSMMSingleCell_1.6.0.tar.gz'
Content type 'application/x-gzip' length 16875718 bytes (16.1 MB)
downloaded 16.1 MB
- installing source package 'HSMMSingleCell' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HSMMSingleCell'
finding HTML links ... 好了
HSMM html
HSMMSingleCell-package html
** building package indices
** installing vignettes
** 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 (HSMMSingleCell)
The downloaded source packages are in
‘C:\Windows\Temp\RtmpwfgZbY\downloaded_packages’
Installation path not writeable, unable to update packages: boot, class,
foreign, lattice, MASS, nlme, nnet, survival
Old packages: 'ade4', 'afex', 'arules', 'backports', 'bayestestR',
'BiocNeighbors', 'BiocSingular', 'biomaRt', 'bit', 'bridgesampling',
'broom', 'broomExtra', 'car', 'checkmate', 'cli', 'crosstalk', 'dendextend',
'DescTools', 'deSolve', 'digest', 'dplyr', 'effectsize', 'emmeans',
'factoextra', 'FactoMineR', 'forcats', 'foreach', 'gameofthrones', 'genefu',
'GenomicFeatures', 'GGally', 'ggfortify', 'ggplot2', 'ggrepel',
'ggstatsplot', 'glue', 'GOSemSim', 'gplots', 'groupedstats', 'gtools',
'harrypotter', 'HDF5Array', 'Hmisc', 'htmltab', 'igraph', 'insight', 'jmv',
'jsonlite', 'lava', 'lifecycle', 'lme4', 'lubridate', 'manipulateWidget',
'metafor', 'mime', 'mnormt', 'modelr', 'modeltools', 'nloptr',
'pairwiseComparisons', 'paletteer', 'parameters', 'pbkrtest', 'performance',
'pkgmaker', 'plotly', 'plyr', 'quantreg', 'qvcalc', 'R.methodsS3',
'rcompanion', 'Rcpp', 'RcppAnnoy', 'RcppParallel', 'rematch2', 'reticulate',
'rgl', 'Rhtslib', 'rJava', 'rlang', 'robust', 'robustbase', 'Rsamtools',
'rstan', 'rsvd', 'rvcheck', 'scater', 'scran', 'Seurat', 'shiny', 'sjmisc',
'sn', 'sp', 'SQUAREM', 'statmod', 'statsExpressions', 'stringi', 'survcomp',
'taRifx', 'tibble', 'tidyr', 'tidyselect', 'tinytex', 'TSP', 'uwot', 'vcd',
'VIM', 'WGCNA', 'yaml', 'zoo'
Update all/some/none? [a/s/n]:
n
library(monocle)
载入需要的程辑包：Biobase
载入需要的程辑包：BiocGenerics
载入需要的程辑包：parallel
载入程辑包：‘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:Matrix’:
which
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, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
载入需要的程辑包：VGAM
载入需要的程辑包：stats4
载入需要的程辑包：splines
载入需要的程辑包：DDRTree
载入需要的程辑包：irlba
Warning messages:
1: 程辑包‘VGAM’是用R版本3.6.3 来建造的
2: 程辑包‘DDRTree’是用R版本3.6.3 来建造的
install.packages('installr')
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/installr_0.22.0.zip'
Content type 'application/zip' length 342565 bytes (334 KB)
downloaded 334 KB
package ‘installr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Windows\Temp\RtmpwfgZbY\downloaded_packages
library(installr)
载入需要的程辑包：stringr
Welcome to installr version 0.22.0
More information is available on the installr project website:
https://github.com/talgalili/installr/
Contact: tal.galili@gmail.com
Suggestions and bug-reports can be submitted at: https://github.com/talgalili/installr/issues
To suppress this message use:
suppressPackageStartupMessages(library(installr))
Warning message:
程辑包‘installr’是用R版本3.6.3 来建造的
install.Rtools()
Loading required namespace: pkgbuild
Failed with error: ‘there is no package called ‘pkgbuild’’
Loading required package: htmltab
No encoding supplied: defaulting to UTF-8.
Argument 'which' was left unspecified. Choosing first table.
Neither <thead> nor <th> information found. Taking first table row for the header. If incorrect, specifiy header argument.
Please remember you are using: R version 3.6.2 (2019-12-12)
trying URL 'https://cran.r-project.org/bin/windows/Rtools/Rtools35.exe'
Content type 'application/x-msdos-program' length 108622512 bytes (103.6 MB)
downloaded 103.6 MB
The file was downloaded successfully into:
C:\WINDOWS\Temp\RtmpwfgZbY/Rtools35.exe
Running the installer now...
Installation status: TRUE . Removing the file:
C:\WINDOWS\Temp\RtmpwfgZbY/Rtools35.exe
(In the future, you may keep the file by setting keep_install_file=TRUE)
