不存在叫‘AnnotationFilter’这个名字的程辑包

不存在叫‘AnnotationFilter’这个名字的程辑包

还是老话，缺啥装啥。

> library(Signac)
Error: package or namespace load failed for ‘Signac’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 不存在叫‘AnnotationFilter’这个名字的程辑包
> BiocManager::install("AnnotationFilter")
Error: Bioconductor version cannot be validated; no internet connection?
> BiocManager::install("AnnotationFilter")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'AnnotationFilter'
trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/AnnotationFilter_1.14.0.zip'
Content type 'application/zip' length 532767 bytes (520 KB)
downloaded 520 KB

package ‘AnnotationFilter’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Nano\AppData\Local\Temp\RtmpAXxgI1\downloaded_packages
Old packages: 'backports', 'bayestestR', 'biomaRt', 'brio', 'broom', 'cachem', 'caTools',
  'cli', 'clusterProfiler', 'coin', 'correlation', 'cpp11', 'crayon', 'crosstalk',
  'data.table', 'DBI', 'dbplyr', 'DelayedArray', 'deldir', 'desc', 'DescTools', 'DESeq2',
  'dplyr', 'e1071', 'edgeR', 'effectsize', 'enrichplot', 'expm', 'fansi', 'farver', 'fastmap',
  'findpython', 'flextable', 'forcats', 'formatR', 'GenomeInfoDb', 'gert', 'ggforce',
  'ggraph', 'ggrepel', 'ggsignif', 'ggstatsplot', 'glmnet', 'GSVA', 'Hmisc', 'hms', 'httpuv',
  'insight', 'ipmisc', 'ipred', 'isoband', 'knitr', 'lava', 'leiden', 'libcoin', 'lifecycle',
  'lubridate', 'maftools', 'magick', 'maptools', 'MASS', 'mathjaxr', 'Matrix',
  'MatrixGenerics', 'MatrixModels', 'matrixStats', 'memoise', 'metaBMA', 'mgcv', 'mime',
  'multcomp', 'nlme', 'officer', 'pairwiseComparisons', 'parallelly', 'parameters',
  'pbkrtest', 'performance', 'pillar', 'pixmap', 'pkgload', 'plotrix', 'PMCMRplus',
  'promises', 'proxy', 'ps', 'quantreg', 'R.devices', 'rappdirs', 'rcompanion', 'Rcpp',
  'RcppArmadillo', 'RcppParallel', 'RCurl', 'Rdpack', 'reprex', 'rio', 'rlang', 'rmarkdown',
  'rms', 'RSQLite', 'rstatix', 'rtracklayer', 'rvest', 'segmented', 'shiny', 'SparseM',
  'spatstat', 'spatstat.data', 'spatstat.utils', 'statsExpressions', 'survival', 'survminer',
  'svglite', 'systemfonts', 'testthat', 'tibble', 'tidyBF', 'tidyr', 'tinytex', 'usethis',
  'utf8', 'waldo', 'WGCNA', 'withr', 'WRS2', 'xfun', 'XML', 'zoo', 'boot', 'class', 'cluster',
  'codetools', 'foreign', 'KernSmooth', 'nnet', 'spatial'
Update all/some/none? [a/s/n]: 
n
> library(Seurat)
> library(Signac)
Error: package or namespace load failed for ‘Signac’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 不存在叫‘biovizBase’这个名字的程辑包
> BiocManager::install("biovizBase")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'biovizBase'
also installing the dependencies ‘ProtGenerics’, ‘dichromat’, ‘GenomicFeatures’, ‘VariantAnnotation’, ‘ensembldb’

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/ProtGenerics_1.22.0.zip'
Content type 'application/zip' length 92552 bytes (90 KB)
downloaded 90 KB

trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/dichromat_2.0-0.zip'
Content type 'application/zip' length 149246 bytes (145 KB)
downloaded 145 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/GenomicFeatures_1.42.2.zip'
Content type 'application/zip' length 2384504 bytes (2.3 MB)
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/VariantAnnotation_1.36.0.zip'
Content type 'application/zip' length 6133985 bytes (5.8 MB)
downloaded 5.8 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/ensembldb_2.14.0.zip'
Content type 'application/zip' length 3533757 bytes (3.4 MB)
downloaded 3.4 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/biovizBase_1.38.0.zip'
Content type 'application/zip' length 2834552 bytes (2.7 MB)
downloaded 2.7 MB

package ‘ProtGenerics’ successfully unpacked and MD5 sums checked
package ‘dichromat’ successfully unpacked and MD5 sums checked
package ‘GenomicFeatures’ successfully unpacked and MD5 sums checked
package ‘VariantAnnotation’ successfully unpacked and MD5 sums checked
package ‘ensembldb’ successfully unpacked and MD5 sums checked
package ‘biovizBase’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Nano\AppData\Local\Temp\RtmpAXxgI1\downloaded_packages
Old packages: 'backports', 'bayestestR', 'biomaRt', 'brio', 'broom', 'cachem', 'caTools',
  'cli', 'clusterProfiler', 'coin', 'correlation', 'cpp11', 'crayon', 'crosstalk',
  'data.table', 'DBI', 'dbplyr', 'DelayedArray', 'deldir', 'desc', 'DescTools', 'DESeq2',
  'dplyr', 'e1071', 'edgeR', 'effectsize', 'enrichplot', 'expm', 'fansi', 'farver', 'fastmap',
  'findpython', 'flextable', 'forcats', 'formatR', 'GenomeInfoDb', 'gert', 'ggforce',
  'ggraph', 'ggrepel', 'ggsignif', 'ggstatsplot', 'glmnet', 'GSVA', 'Hmisc', 'hms', 'httpuv',
  'insight', 'ipmisc', 'ipred', 'isoband', 'knitr', 'lava', 'leiden', 'libcoin', 'lifecycle',
  'lubridate', 'maftools', 'magick', 'maptools', 'MASS', 'mathjaxr', 'Matrix',
  'MatrixGenerics', 'MatrixModels', 'matrixStats', 'memoise', 'metaBMA', 'mgcv', 'mime',
  'multcomp', 'nlme', 'officer', 'pairwiseComparisons', 'parallelly', 'parameters',
  'pbkrtest', 'performance', 'pillar', 'pixmap', 'pkgload', 'plotrix', 'PMCMRplus',
  'promises', 'proxy', 'ps', 'quantreg', 'R.devices', 'rappdirs', 'rcompanion', 'Rcpp',
  'RcppArmadillo', 'RcppParallel', 'RCurl', 'Rdpack', 'reprex', 'rio', 'rlang', 'rmarkdown',
  'rms', 'RSQLite', 'rstatix', 'rtracklayer', 'rvest', 'segmented', 'shiny', 'SparseM',
  'spatstat', 'spatstat.data', 'spatstat.utils', 'statsExpressions', 'survival', 'survminer',
  'svglite', 'systemfonts', 'testthat', 'tibble', 'tidyBF', 'tidyr', 'tinytex', 'usethis',
  'utf8', 'waldo', 'WGCNA', 'withr', 'WRS2', 'xfun', 'XML', 'zoo', 'boot', 'class', 'cluster',
  'codetools', 'foreign', 'KernSmooth', 'nnet', 'spatial'
Update all/some/none? [a/s/n]: 
Update all/some/none? [a/s/n]: 
n
> library(Signac)
Error: package or namespace load failed for 'Signac' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 不存在叫'ggbio'这个名字的程辑包
> BiocManager::install("ggbio")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'ggbio'
also installing the dependency 'OrganismDbi'

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/OrganismDbi_1.32.0.zip'
Content type 'application/zip' length 671430 bytes (655 KB)
downloaded 655 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/ggbio_1.38.0.zip'
Content type 'application/zip' length 3537448 bytes (3.4 MB)
downloaded 3.4 MB

package 'OrganismDbi' successfully unpacked and MD5 sums checked
package 'ggbio' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Nano\AppData\Local\Temp\RtmpAXxgI1\downloaded_packages
Old packages: 'backports', 'bayestestR', 'biomaRt', 'brio', 'broom', 'cachem', 'caTools',
  'cli', 'clusterProfiler', 'coin', 'correlation', 'cpp11', 'crayon', 'crosstalk',
  'data.table', 'DBI', 'dbplyr', 'DelayedArray', 'deldir', 'desc', 'DescTools', 'DESeq2',
  'dplyr', 'e1071', 'edgeR', 'effectsize', 'enrichplot', 'expm', 'fansi', 'farver', 'fastmap',
  'findpython', 'flextable', 'forcats', 'formatR', 'GenomeInfoDb', 'gert', 'ggforce',
  'ggraph', 'ggrepel', 'ggsignif', 'ggstatsplot', 'glmnet', 'GSVA', 'Hmisc', 'hms', 'httpuv',
  'insight', 'ipmisc', 'ipred', 'isoband', 'knitr', 'lava', 'leiden', 'libcoin', 'lifecycle',
  'lubridate', 'maftools', 'magick', 'maptools', 'MASS', 'mathjaxr', 'Matrix',
  'MatrixGenerics', 'MatrixModels', 'matrixStats', 'memoise', 'metaBMA', 'mgcv', 'mime',
  'multcomp', 'nlme', 'officer', 'pairwiseComparisons', 'parallelly', 'parameters',
  'pbkrtest', 'performance', 'pillar', 'pixmap', 'pkgload', 'plotrix', 'PMCMRplus',
  'promises', 'proxy', 'ps', 'quantreg', 'R.devices', 'rappdirs', 'rcompanion', 'Rcpp',
  'RcppArmadillo', 'RcppParallel', 'RCurl', 'Rdpack', 'reprex', 'rio', 'rlang', 'rmarkdown',
  'rms', 'RSQLite', 'rstatix', 'rtracklayer', 'rvest', 'segmented', 'shiny', 'SparseM',
  'spatstat', 'spatstat.data', 'spatstat.utils', 'statsExpressions', 'survival', 'survminer',
  'svglite', 'systemfonts', 'testthat', 'tibble', 'tidyBF', 'tidyr', 'tinytex', 'usethis',
  'utf8', 'waldo', 'WGCNA', 'withr', 'WRS2', 'xfun', 'XML', 'zoo', 'boot', 'class', 'cluster',
  'codetools', 'foreign', 'KernSmooth', 'nnet', 'spatial'
Update all/some/none? [a/s/n]: 
Update all/some/none? [a/s/n]: 
n
> library(Signac)
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

载入程辑包：'Signac'

The following object is masked from 'package:Seurat':

    FoldChange

好了

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