{"id":2454,"date":"2020-06-22T12:33:42","date_gmt":"2020-06-22T03:33:42","guid":{"rendered":"https:\/\/plaza.umin.ac.jp\/~OIO\/?p=2454"},"modified":"2020-06-22T12:38:21","modified_gmt":"2020-06-22T03:38:21","slug":"biocmanager-bioconuctor-%e3%81%ae%e3%82%a2%e3%83%83%e3%83%97%e3%83%87%e3%83%bc%e3%83%88","status":"publish","type":"post","link":"https:\/\/plaza.umin.ac.jp\/~OIO\/?p=2454","title":{"rendered":"BiocManager, Bioconductor \u306e\u30a2\u30c3\u30d7\u30c7\u30fc\u30c8"},"content":{"rendered":"<p>Bioconductor\u3092\u30a2\u30c3\u30d7\u30c7\u30fc\u30c8\u3057\u3088\u3046\u3068\u3057\u305f\u306e\u3067\u3059\u304c\u3001\u73fe\u6642\u70b9\u306e\u6700\u65b0\u30d0\u30fc\u30b8\u30e7\u30f33.11\u306f\u3001R\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u304c\u3061\u3087\u3053\u3063\u3068\u53e4\u304f\u3066\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3067\u304d\u307e\u305b\u3093\u3002\u305d\u3053\u3067\u30013.10\u3092\u5165\u308c\u308b\u3053\u3068\u306b\u3057\u307e\u3057\u305f\u3002\u4ee5\u4e0b\u306f\u305d\u306e\u6642\u306e\u30ed\u30b0\u3067\u3001\u30a8\u30e9\u30fc\u3067\u306f\u3058\u304b\u308c\u308b\u3068\u3053\u308d\u3082\u542b\u3081\u3066\u63b2\u8f09\u3067\u3059\u3002\uff08win\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u540d\u3060\u3051\u5909\u66f4\u3057\u3066\u3044\u307e\u3059\uff09<\/p>\n<p><font face=\"Bahnschrift Light\">[Workspace loaded from ~\/.RData]<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><font color=\"#0000ff\"><u><strong>&gt; library(BiocManager)<\/strong><\/u><\/font><br \/>\nBioconductor version 3.9 (BiocManager 1.30.10), ?BiocManager::install for help<br \/>\nBioconductor version &#8216;3.9&#8217; is out-of-date; the current release version &#8216;3.11&#8217;<br \/>&nbsp;&nbsp; is available with R version &#8216;4.0&#8217;; see <\/font><a href=\"https:\/\/bioconductor.org\/install\"><font face=\"Bahnschrift Light\">https:\/\/bioconductor.org\/install<\/font><\/a><br \/><font face=\"Bahnschrift Light\">&nbsp; \u8b66\u544a\u30e1\u30c3\u30bb\u30fc\u30b8: <br \/>&nbsp; \u30d1\u30c3\u30b1\u30fc\u30b8 \u2018BiocManager\u2019 \u306f\u30d0\u30fc\u30b8\u30e7\u30f3 3.6.3 \u306e R \u306e\u4e0b\u3067\u9020\u3089\u308c\u307e\u3057\u305f&nbsp; <br \/><font color=\"#0000ff\"><strong><u><br \/>\n&gt; BiocManager::install(version = &#8220;3.11&#8221;)<\/u><\/strong><\/font><br \/>&nbsp; \u30a8\u30e9\u30fc: Bioconductor version &#8216;3.11&#8217; requires R version &#8216;4.0&#8217;; see<br \/>&nbsp;&nbsp; <\/font><a href=\"https:\/\/bioconductor.org\/install\"><font face=\"Bahnschrift Light\">https:\/\/bioconductor.org\/install<\/font><\/a><br \/><font face=\"Bahnschrift Light\"><br \/>\n&gt; BiocManager::install(version = &#8220;3.10&#8221;)<br \/>\nUpgrade 195 packages to Bioconductor version &#8216;3.10&#8217;? [y\/n]: <br \/>\ny<br \/>\nBioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)<br \/>\nInstalling package(s) &#8216;BiocVersion&#8217;<br \/>&nbsp; URL &#8216;<\/font><a href=\"https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/BiocVersion_3.10.1.zip'\"><font face=\"Bahnschrift Light\">https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/BiocVersion_3.10.1.zip&#8217;<\/font><\/a><font face=\"Bahnschrift Light\"> \u3092\u8a66\u3057\u3066\u3044\u307e\u3059 <br \/>\nContent type &#8216;application\/zip&#8217; length 8903 bytes<br \/>\ndownloaded 8903 bytes<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\">package \u2018BiocVersion\u2019 successfully unpacked and MD5 sums checked<br \/>&nbsp; unpackPkgZip(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib, libs_only,&nbsp; \u3067\u30a8\u30e9\u30fc: <br \/>&nbsp;&nbsp; ERROR: failed to lock directory \u2018C:\\Users\\my_username\\Documents\\R\\win-library\\3.6\u2019 for modifying<br \/>\nTry removing \u2018C:\\Users\\my_username\\Documents\\R\\win-library\\3.6\/00LOCK\u2019<br \/>&nbsp; \u8ffd\u52a0\u60c5\u5831:&nbsp; \u8b66\u544a\u30e1\u30c3\u30bb\u30fc\u30b8: <br \/>\n1:&nbsp; readChar(&#8230;) \u3067: <br \/>&nbsp;&nbsp;&nbsp; UTF-8 \u4ee5\u5916\u306e\u30de\u30eb\u30c1\u30d0\u30a4\u30c8\u30ed\u30b1\u30fc\u30eb\u3067\u306f\u30d0\u30a4\u30c8\u578b\u3067\u306e\u307f\u8aad\u307f\u8fbc\u307f\u53ef\u80fd\u3067\u3059 <br \/>\n2:&nbsp; readChar(&#8230;) \u3067: <br \/>&nbsp;&nbsp;&nbsp; UTF-8 \u4ee5\u5916\u306e\u30de\u30eb\u30c1\u30d0\u30a4\u30c8\u30ed\u30b1\u30fc\u30eb\u3067\u306f\u30d0\u30a4\u30c8\u578b\u3067\u306e\u307f\u8aad\u307f\u8fbc\u307f\u53ef\u80fd\u3067\u3059 <br \/>\n3:&nbsp; readChar(&#8230;) \u3067: <br \/>&nbsp;&nbsp;&nbsp; UTF-8 \u4ee5\u5916\u306e\u30de\u30eb\u30c1\u30d0\u30a4\u30c8\u30ed\u30b1\u30fc\u30eb\u3067\u306f\u30d0\u30a4\u30c8\u578b\u3067\u306e\u307f\u8aad\u307f\u8fbc\u307f\u53ef\u80fd\u3067\u3059 <br \/>\n4:&nbsp; readChar(&#8230;) \u3067: <br \/>&nbsp;&nbsp;&nbsp; UTF-8 \u4ee5\u5916\u306e\u30de\u30eb\u30c1\u30d0\u30a4\u30c8\u30ed\u30b1\u30fc\u30eb\u3067\u306f\u30d0\u30a4\u30c8\u578b\u3067\u306e\u307f\u8aad\u307f\u8fbc\u307f\u53ef\u80fd\u3067\u3059 <br \/>\n5:&nbsp; readChar(&#8230;) \u3067: <br \/>&nbsp;&nbsp;&nbsp; UTF-8 \u4ee5\u5916\u306e\u30de\u30eb\u30c1\u30d0\u30a4\u30c8\u30ed\u30b1\u30fc\u30eb\u3067\u306f\u30d0\u30a4\u30c8\u578b\u3067\u306e\u307f\u8aad\u307f\u8fbc\u307f\u53ef\u80fd\u3067\u3059 <br \/><font color=\"#0000ff\"><strong><u><br \/>\n&gt; BiocManager::install(version = &#8220;3.10&#8221;)<\/u><\/strong><\/font><br \/>\nUpgrade 195 packages to Bioconductor version &#8216;3.10&#8217;? [y\/n]: <br \/>\ny<br \/>\nBioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)<br \/>\nInstalling package(s) &#8216;BiocVersion&#8217;<br \/>&nbsp; URL &#8216;<\/font><a href=\"https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/BiocVersion_3.10.1.zip'\"><font face=\"Bahnschrift Light\">https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/BiocVersion_3.10.1.zip&#8217;<\/font><\/a><font face=\"Bahnschrift Light\"> \u3092\u8a66\u3057\u3066\u3044\u307e\u3059 <br \/>\nContent type &#8216;application\/zip&#8217; length 8903 bytes<br \/>\ndownloaded 8903 bytes<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\">package \u2018BiocVersion\u2019 successfully unpacked and MD5 sums checked<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\">The downloaded binary packages are in<br \/>&nbsp;&nbsp;&nbsp;&nbsp; C:\\Users\\my_username\\AppData\\Local\\Temp\\RtmpQhgRhw\\downloaded_packages<br \/>\nInstalling package(s) &#8216;wordcloud2&#8217;, &#8216;annotate&#8217;, &#8216;AnnotationDbi&#8217;, &#8216;backports&#8217;,<br \/>&nbsp;&nbsp; &#8216;BH&#8217;, &#8216;Biobase&#8217;, &#8216;BiocGenerics&#8217;, &#8216;BiocParallel&#8217;, &#8216;BiocVersion&#8217;, &#8216;bit&#8217;,<br \/>&nbsp;&nbsp; &#8216;blob&#8217;, &#8216;broom&#8217;, &#8216;Cairo&#8217;, &#8216;callr&#8217;, &#8216;car&#8217;, &#8216;carData&#8217;, &#8216;caTools&#8217;, &#8216;checkmate&#8217;,<br \/>&nbsp;&nbsp; &#8216;classInt&#8217;, &#8216;cli&#8217;, &#8216;covr&#8217;, &#8216;crosstalk&#8217;, &#8216;curl&#8217;, &#8216;data.table&#8217;, &#8216;DBI&#8217;,<br \/>&nbsp;&nbsp; &#8216;dbplyr&#8217;, &#8216;DelayedArray&#8217;, &#8216;DESeq2&#8217;, &#8216;devtools&#8217;, &#8216;DiagrammeR&#8217;, &#8216;digest&#8217;,<br \/>&nbsp;&nbsp; &#8216;dplyr&#8217;, &#8216;drat&#8217;, &#8216;DT&#8217;, &#8216;edgeR&#8217;, &#8216;ellipsis&#8217;, &#8216;epiR&#8217;, &#8216;fansi&#8217;, &#8216;farver&#8217;,<br \/>&nbsp;&nbsp; &#8216;fitdistrplus&#8217;, &#8216;forcats&#8217;, &#8216;foreach&#8217;, &#8216;forecast&#8217;, &#8216;fracdiff&#8217;, &#8216;fs&#8217;, &#8216;gargle&#8217;,<br \/>&nbsp;&nbsp; &#8216;genefilter&#8217;, &#8216;geneplotter&#8217;, &#8216;GenomeInfoDb&#8217;, &#8216;GenomeInfoDbData&#8217;,<br \/>&nbsp;&nbsp; &#8216;GenomicRanges&#8217;, &#8216;GEOmetadb&#8217;, &#8216;GEOquery&#8217;, &#8216;ggplot2&#8217;, &#8216;ggpubr&#8217;, &#8216;ggrepel&#8217;,<br \/>&nbsp;&nbsp; &#8216;gh&#8217;, &#8216;git2r&#8217;, &#8216;glue&#8217;, &#8216;GO.db&#8217;, &#8216;googleAuthR&#8217;, &#8216;googledrive&#8217;,<br \/>&nbsp;&nbsp; &#8216;googlesheets4&#8217;, &#8216;gplots&#8217;, &#8216;gtools&#8217;, &#8216;h2o&#8217;, &#8216;haven&#8217;, &#8216;Heatplus&#8217;, &#8216;hexbin&#8217;,<br \/>&nbsp;&nbsp; &#8216;Hmisc&#8217;, &#8216;hms&#8217;, &#8216;htmlTable&#8217;, &#8216;htmltools&#8217;, &#8216;httpuv&#8217;, &#8216;igraph&#8217;, &#8216;imager&#8217;,<br \/>&nbsp;&nbsp; &#8216;IRanges&#8217;, &#8216;ISOcodes&#8217;, &#8216;jomo&#8217;, &#8216;jsonlite&#8217;, &#8216;knitr&#8217;, &#8216;labelled&#8217;, &#8216;lamW&#8217;,<br \/>&nbsp;&nbsp; &#8216;later&#8217;, &#8216;latticeExtra&#8217;, &#8216;LBE&#8217;, &#8216;lifecycle&#8217;, &#8216;limma&#8217;, &#8216;lme4&#8217;, &#8216;lmerTest&#8217;,<br \/>&nbsp;&nbsp; &#8216;locfit&#8217;, &#8216;lubridate&#8217;, &#8216;maptools&#8217;, &#8216;matrixStats&#8217;, &#8216;mcmc&#8217;, &#8216;MCMCpack&#8217;,<br \/>&nbsp;&nbsp; &#8216;MetaIntegrator&#8217;, &#8216;mice&#8217;, &#8216;mime&#8217;, &#8216;modelr&#8217;, &#8216;modeltools&#8217;, &#8216;multtest&#8217;,<br \/>&nbsp;&nbsp; &#8216;mvtnorm&#8217;, &#8216;nloptr&#8217;, &#8216;openxlsx&#8217;, &#8216;ordinal&#8217;, &#8216;org.Hs.eg.db&#8217;, &#8216;pbkrtest&#8217;,<br \/>&nbsp;&nbsp; &#8216;pillar&#8217;, &#8216;pkgbuild&#8217;, &#8216;pkgload&#8217;, &#8216;plotly&#8217;, &#8216;plyr&#8217;, &#8216;pracma&#8217;,<br \/>&nbsp;&nbsp; &#8216;preprocessCore&#8217;, &#8216;prettyunits&#8217;, &#8216;pROC&#8217;, &#8216;processx&#8217;, &#8216;promises&#8217;, &#8216;ps&#8217;,<br \/>&nbsp;&nbsp; &#8216;purrr&#8217;, &#8216;quantmod&#8217;, &#8216;quantreg&#8217;, &#8216;R.methodsS3&#8217;, &#8216;raster&#8217;, &#8216;Rcpp&#8217;,<br \/>&nbsp;&nbsp; &#8216;RcppArmadillo&#8217;, &#8216;RcppEigen&#8217;, &#8216;RcppParallel&#8217;, &#8216;RcppProgress&#8217;, &#8216;RCurl&#8217;,<br \/>&nbsp;&nbsp; &#8216;rematch2&#8217;, &#8216;remotes&#8217;, &#8216;reshape2&#8217;, &#8216;rex&#8217;, &#8216;rgdal&#8217;, &#8216;rgexf&#8217;, &#8216;rgl&#8217;, &#8216;rlang&#8217;,<br \/>&nbsp;&nbsp; &#8216;rmarkdown&#8217;, &#8216;RMySQL&#8217;, &#8216;ROCit&#8217;, &#8216;ROCR&#8217;, &#8216;roxygen2&#8217;, &#8216;RSpectra&#8217;, &#8216;RSQLite&#8217;,<br \/>&nbsp;&nbsp; &#8216;rstudioapi&#8217;, &#8216;rversions&#8217;, &#8216;S4Vectors&#8217;, &#8216;scales&#8217;, &#8216;selectr&#8217;, &#8216;seqminer&#8217;,<br \/>&nbsp;&nbsp; &#8216;SeqNet&#8217;, &#8216;sf&#8217;, &#8216;shiny&#8217;, &#8216;SKAT&#8217;, &#8216;slam&#8217;, &#8216;sn&#8217;, &#8216;sp&#8217;, &#8216;SparseM&#8217;, &#8216;spatstat&#8217;,<br \/>&nbsp;&nbsp; &#8216;spData&#8217;, &#8216;statmod&#8217;, &#8216;stopwords&#8217;, &#8216;stringi&#8217;, &#8216;SummarizedExperiment&#8217;,<br \/>&nbsp;&nbsp; &#8216;surveillance&#8217;, &#8216;survey&#8217;, &#8216;tableone&#8217;, &#8216;testthat&#8217;, &#8216;text2vec&#8217;, &#8216;tibble&#8217;,<br \/>&nbsp;&nbsp; &#8216;tidyr&#8217;, &#8216;tidyselect&#8217;, &#8216;tidyverse&#8217;, &#8216;tinytex&#8217;, &#8216;tm&#8217;, &#8216;topicmodels&#8217;, &#8216;TTR&#8217;,<br \/>&nbsp;&nbsp; &#8216;units&#8217;, &#8216;usethis&#8217;, &#8216;uuid&#8217;, &#8216;vctrs&#8217;, &#8216;visNetwork&#8217;, &#8216;withr&#8217;, &#8216;xfun&#8217;,<br \/>&nbsp;&nbsp; &#8216;xgboost&#8217;, &#8216;XML&#8217;, &#8216;xml2&#8217;, &#8216;xts&#8217;, &#8216;XVector&#8217;, &#8216;yaml&#8217;, &#8216;zlibbioc&#8217;, &#8216;zoo&#8217;<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\">&nbsp; There are binary versions available but the source versions are later:<br \/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; binary source needs_compilation<br \/>\nbackports&nbsp; 1.1.7&nbsp; 1.1.8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; TRUE<br \/>\nhtmlTable 1.13.3&nbsp; 2.0.0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; FALSE<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"> URL &#8216;<\/font><a href=\"https:\/\/cran.rstudio.com\/bin\/windows\/contrib\/3.6\/wordcloud2_0.2.1.zip'\"><font face=\"Bahnschrift Light\">https:\/\/cran.rstudio.com\/bin\/windows\/contrib\/3.6\/wordcloud2_0.2.1.zip&#8217;<\/font><\/a><font face=\"Bahnschrift Light\"> \u3092\u8a66\u3057\u3066\u3044\u307e\u3059 <br \/>\nContent type &#8216;application\/zip&#8217; length 999844 bytes (976 KB)<br \/>\ndownloaded 976 KB<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"> URL &#8216;<\/font><a href=\"https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/annotate_1.64.0.zip'\"><font face=\"Bahnschrift Light\">https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/annotate_1.64.0.zip&#8217;<\/font><\/a><font face=\"Bahnschrift Light\"> \u3092\u8a66\u3057\u3066\u3044\u307e\u3059 <br \/>\nContent type &#8216;application\/zip&#8217; length 2238722 bytes (2.1 MB)<br \/>\ndownloaded 2.1 MB<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"> URL &#8216;<\/font><a href=\"https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/AnnotationDbi_1.48.0.zip'\"><font face=\"Bahnschrift Light\">https:\/\/bioconductor.org\/packages\/3.10\/bioc\/bin\/windows\/contrib\/3.6\/AnnotationDbi_1.48.0.zip&#8217;<\/font><\/a><font face=\"Bahnschrift Light\"> \u3092\u8a66\u3057\u3066\u3044\u307e\u3059 <br \/>\nContent type &#8216;application\/zip&#8217; length 5226197 bytes (5.0 MB)<br \/>\ndownloaded 5.0 MB<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"><br \/>\n<\/font><\/p>\n<p><font face=\"Bahnschrift Light\"> URL &#8216;<\/font><a href=\"https:\/\/cran.rstudio.com\/bin\/windows\/contrib\/3.6\/BH_1.72.0-3.zip'\"><font face=\"Bahnschrift Light\">https:\/\/cran.rstudio.com\/bin\/windows\/contrib\/3.6\/BH_1.72.0-3.zip&#8217;<\/font><\/a><font face=\"Bahnschrift Light\"> \u3092\u8a66\u3057\u3066\u3044\u307e\u3059 <br \/>\nContent type &#8216;application\/zip&#8217; 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