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WGCNAインストールログ

参照ページ https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/(external link)


(1)WGCNAのインストール
  • WGCNAのインストールで、ミラーサイト選択のところで「18: (HTTP mirrors)」を選び、その次に「48: Japan (Tokyo)」を選ぶのがポイント!
$ /install_path/R-3.2.2/bin/R
 ...snip...
> source("http://bioconductor.org/biocLite.R") 
> biocLite(c("AnnotationDbi", "impute", "GO.db", "preprocessCore")) 
> install.packages("WGCNA")
> install.packages("WGCNA")
 --- このセッションで使うために、CRAN のミラーサイトを選んでください ---
Error in download.file(url, destfile = f, quiet = TRUE) :
   サポートされていないURLスキームです
HTTPS CRAN mirror

 1: 0-Cloud [https]             2: Austria [https]
 3: China (Beijing 4) [https]   4: China (Hefei) [https]
 5: Colombia (Cali) [https]     6: France (Lyon 2) [https]
 7: Iceland [https]             8: Russia (Moscow 1) [https]
 9: Switzerland [https]        10: UK (Bristol) [https]
11: UK (Cambridge) [https]     12: USA (CA 1) [https]
13: USA (KS) [https]           14: USA (MI 1) [https]
15: USA (TN) [https]           16: USA (TX) [https]
17: USA (WA) [https]           18: (HTTP mirrors)

Selection: 18
HTTP CRAN mirror

  1: 0-Cloud                        2: Algeria
  3: Argentina (La Plata)           4: Australia (Canberra)
  5: Australia (Melbourne)          6: Austria
  7: Belgium                        8: Brazil (BA)
  9: Brazil (PR)                   10: Brazil (RJ)
 11: Brazil (SP 1)                 12: Brazil (SP 2)
 13: Canada (BC)                   14: Canada (NS)
 15: Canada (ON)                   16: Canada (QC 1)
 17: Canada (QC 2)                 18: Chile
 19: China (Beijing 2)             20: China (Beijing 3)
 21: China (Beijing 4)             22: China (Hefei)
 23: China (Xiamen)                24: Colombia (Cali)
 25: Czech Republic                26: Denmark
 27: Ecuador                       28: El Salvador
 29: Estonia                       30: France (Lyon 1)
 31: France (Lyon 2)               32: France (Montpellier)
 33: France (Paris 2)              34: Germany (Berlin)
 35: Germany (Gottingen)          36: Germany (Frankfurt)
 37: Germany (Munster)            38: Greece
 39: Hungary                       40: Iceland
 41: India                         42: Indonesia (Jakarta)
 43: Iran                          44: Ireland
 45: Italy (Milano)                46: Italy (Padua)
 47: Italy (Palermo)               48: Japan (Tokyo)
 49: Japan (Yamagata)              50: Korea (Seoul 1)
 51: Korea (Seoul 2)               52: Korea (Ulsan)
 53: Lebanon                       54: Mexico (Mexico City)
 55: Mexico (Texcoco)              56: Netherlands (Amsterdam)
 57: Netherlands (Utrecht)         58: New Zealand
 59: Norway                        60: Philippines
 61: Poland                        62: Portugal
 63: Russia (Moscow 1)             64: Russia (Moscow 2)
 65: Slovakia                      66: South Africa (Johannesburg)
 67: Spain (A Coruna)             68: Spain (Madrid)
 69: Sweden                        70: Switzerland
 71: Taiwan (Chungli)              72: Taiwan (Taipei)
 73: Thailand                      74: Turkey
 75: UK (Bristol)                  76: UK (Cambridge)
 77: UK (Hampshire)                78: UK (London 1)
 79: UK (London 2)                 80: UK (St Andrews)
 81: USA (CA 1)                    82: USA (CA 2)
 83: USA (CO)                      84: USA (IA)
 85: USA (IN)                      86: USA (KS)
 87: USA (MD)                      88: USA (MI 1)
 89: USA (MI 2)                    90: USA (MO)
 91: USA (NC)                      92: USA (OH 1)
 93: USA (OH 2)                    94: USA (OR)
 95: USA (PA 1)                    96: USA (PA 2)
 97: USA (TN)                      98: USA (TX)
 99: USA (WA)                     100: Venezuela
101: Vietnam

Selection: 48
...snip...
==========================================================================
*
*  Package WGCNA 1.51 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R.
*    To allow multi-threading within WGCNA with all available cores, use
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example
*
*          ALLOW_WGCNA_THREADS=16
*
*    To set the environment variable in linux bash shell, type
*
*           export ALLOW_WGCNA_THREADS=16
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


* DONE (WGCNA)

 ダウンロードされたパッケージは、以下にあります
        ‘/tmp/Rtmpqeg5PZ/downloaded_packages’
 '.Library' 中のパッケージの HTML 索引を更新します
Making 'packages.html' ...  完了


Last edited by nomonma .
Page last modified on 月曜日 21 of November, 2016 15:59:32 JST.