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0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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16
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3 <package name="libcurl" version="7.35">
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31
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4 <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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16
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5 </package>
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22
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6 <package name="R" version="3.2.1">
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7 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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19
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8 </package>
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1
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9 <package name="450kdependency" version="0.0.1">
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3
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10 <install version="1.0">
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4
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11 <actions>
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12
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12 <action type="setup_r_environment">
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13 <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
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16
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14 <package name="libcurl" version="7.35" />
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15 </repository>
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31
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16 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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22
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17 <package name="R" version="3.2.1" />
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12
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18 </repository>
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110
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19 <action type="shell_command">
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20 sudo apt-get install xorg </action>
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21 <action type="shell_command">
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22 sudo apt-get install libx11-dev </action>
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23 <action type="shell_command">
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24 sudo apt-get install r-cran-rgl </action>
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74
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25 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz</package>
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47
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26 <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.36.1.tar.gz</package>
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31
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27 <package>https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz</package>
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28 <package>https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz</package>
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47
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29 <package>https://cran.rstudio.com/src/contrib/locfit_1.5-9.1.tar.gz</package>
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30 <package>https://cran.rstudio.com/src/contrib/matrixStats_0.52.2.tar.gz</package>
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31 <package>http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.32.2.tar.gz</package>
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32 <package>https://cran.r-project.org/src/contrib/registry_0.3.tar.gz</package>
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33 <package>https://cran.r-project.org/src/contrib/digest_0.6.12.tar.gz</package>
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34 <package>https://cran.r-project.org/src/contrib/stringi_1.1.5.tar.gz</package>
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35 <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
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47
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36 <package>https://cran.r-project.org/src/contrib/stringr_1.2.0.tar.gz</package>
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37 <package>https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz</package>
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38 <package>https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz</package>
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39 <package>https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz</package>
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40 <package>https://cran.r-project.org/src/contrib/doRNG_1.6.6.tar.gz</package>
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41 <package>https://cran.r-project.org/src/contrib/DBI_0.6-1.tar.gz</package>
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58
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42 <package>https://cran.r-project.org/src/contrib/memoise_1.1.0.tar.gz</package>
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43 <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.10.tar.gz</package>
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44 <package>https://cran.r-project.org/src/contrib/BH_1.62.0-1.tar.gz</package>
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45 <package>https://cran.r-project.org/src/contrib/plogr_0.1-1.tar.gz</package>
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47
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46 <package>https://cran.r-project.org/src/contrib/RSQLite_1.1-2.tar.gz</package>
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47 <package>https://cran.r-project.org/src/contrib/bitops_1.0-6.tar.gz</package>
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79
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48 <package>https://cran.r-project.org/src/contrib/Archive/RCurl/RCurl_1.95-4.5.tar.gz</package>
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49 <package>https://cran.r-project.org/src/contrib/Archive/XML/XML_3.98-1.2.tar.gz</package>
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61
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50 <package>https://cran.r-project.org/src/contrib/lambda.r_1.1.9.tar.gz</package>
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51 <package>https://cran.r-project.org/src/contrib/futile.options_1.0.0.tar.gz</package>
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60
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52 <package>https://cran.r-project.org/src/contrib/futile.logger_1.4.3.tar.gz</package>
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53 <package>https://cran.r-project.org/src/contrib/snow_0.4-2.tar.gz</package>
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47
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54 <package>http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.10.1.tar.gz</package>
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55 <package>https://cran.r-project.org/src/contrib/lattice_0.20-35.tar.gz</package>
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65
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56 <package>https://cran.r-project.org/src/contrib/openssl_0.9.6.tar.gz</package>
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57 <package>https://cran.r-project.org/src/contrib/base64_2.0.tar.gz</package>
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58 <package>https://cran.r-project.org/src/contrib/quadprog_1.5-5.tar.gz</package>
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66
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59 <package>http://bioconductor.org/packages/release/bioc/src/contrib/multtest_2.32.0.tar.gz</package>
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60 <package>http://bioconductor.org/packages/release/bioc/src/contrib/siggenes_1.50.0.tar.gz</package>
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31
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61 <package>https://cran.r-project.org/src/contrib/Matrix_1.2-10.tar.gz</package>
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62 <package>https://cran.r-project.org/src/contrib/R6_2.2.0.tar.gz</package>
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63 <package>https://cran.r-project.org/src/contrib/nlme_3.1-131.tar.gz</package>
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64 <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
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65 <package>https://cran.r-project.org/src/contrib/nor1mix_1.2-2.tar.gz</package>
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66 <package>https://cran.r-project.org/src/contrib/data.table_1.10.4.tar.gz</package>
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67 <package>https://cran.r-project.org/src/contrib/mclust_5.2.3.tar.gz</package>
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68 <package>https://cran.r-project.org/src/contrib/survival_2.41-3.tar.gz</package>
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69 <package>https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz</package>
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70 <package>https://cran.r-project.org/src/contrib/codetools_0.2-15.tar.gz</package>
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71 <package>http://bioconductor.org/packages/release/bioc/src/contrib/illuminaio_0.18.0.tar.gz</package>
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69
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72 <package>https://cran.r-project.org/src/contrib/jsonlite_1.4.tar.gz</package>
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73 <package>https://cran.r-project.org/src/contrib/mime_0.5.tar.gz</package>
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74 <package>https://cran.r-project.org/src/contrib/curl_2.6.tar.gz</package>
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75 <package>https://cran.r-project.org/src/contrib/httr_1.2.1.tar.gz</package>
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76 <package>ftp://164.41.45.6/pub/plan/R/src/contrib/beanplot_1.2.tar.gz</package>
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77 <package>http://bioconductor.org/packages/release/bioc/src/contrib/preprocessCore_1.38.0.tar.gz</package>
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78 <package>http://bioconductor.org/packages/release/bioc/src/contrib/GEOquery_2.42.0.tar.gz</package>
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79 <package>https://cran.r-project.org/src/contrib/MASS_7.3-47.tar.gz</package>
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80 <package>https://cran.r-project.org/src/contrib/reshape_0.8.6.tar.gz</package>
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73
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81 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/S4Vectors_0.8.11.tar.gz</package>
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53
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82 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/IRanges_2.4.8.tar.gz</package>
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74
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83 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomeInfoDb_1.6.3.tar.gz</package>
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75
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84 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/AnnotationDbi_1.32.3.tar.gz</package>
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85 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/annotate_1.48.0.tar.gz</package>
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76
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86 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/genefilter_1.52.1.tar.gz</package>
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87 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/zlibbioc_1.16.0.tar.gz</package>
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55
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88 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/XVector_0.10.0.tar.gz</package>
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89 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/Biostrings_2.38.4.tar.gz</package>
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54
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90 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.22.4.tar.gz</package>
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76
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91 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/Rsamtools_1.22.0.tar.gz</package>
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92 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/SummarizedExperiment_1.0.2.tar.gz</package>
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93 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicAlignments_1.6.3.tar.gz</package>
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94 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/rtracklayer_1.30.4.tar.gz</package>
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95 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/biomaRt_2.26.1.tar.gz</package>
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96 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicFeatures_1.22.13.tar.gz</package>
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97 <package>https://cran.r-project.org/src/contrib/lattice_0.20-35.tar.gz</package>
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98 <package>https://cran.r-project.org/src/contrib/Archive/irlba/irlba_1.0.3.tar.gz</package>
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99 <package>https://cran.r-project.org/src/contrib/Archive/htmltools/htmltools_0.2.6.tar.gz</package>
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100 <package>https://cran.r-project.org/src/contrib/Archive/RJSONIO/RJSONIO_1.2-0.2.tar.gz</package>
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101 <package>https://cran.r-project.org/src/contrib/Archive/yaml/yaml_2.1.12.tar.gz</package>
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85
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102 <package>https://cran.r-project.org/src/contrib/Archive/htmlwidgets/htmlwidgets_0.3.2.tar.gz</package>
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87
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103 <package>https://cran.rstudio.com/src/contrib/Archive/evaluate/evaluate_0.5.5.tar.gz</package>
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104 <package>https://cran.r-project.org/src/contrib/Archive/formatR/formatR_1.0.tar.gz</package>
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105 <package>https://cran.r-project.org/src/contrib/Archive/highr/highr_0.4.tar.gz</package>
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106 <package>https://cran.r-project.org/src/contrib/Archive/markdown/markdown_0.6.5.tar.gz</package>
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107 <package>https://cran.r-project.org/src/contrib/Archive/knitr/knitr_1.8.tar.gz</package>
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108 <package>https://cran.r-project.org/src/contrib/Archive/httpuv/httpuv_1.2.2.tar.gz</package>
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109 <package>https://cran.r-project.org/src/contrib/Archive/shiny/shiny_0.10.2.tar.gz</package>
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110 <package>https://cran.rstudio.com/src/contrib/ellipse_0.3-8.tar.gz</package>
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111 <package>https://cran.rstudio.com/src/contrib/corpcor_1.6.9.tar.gz</package>
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112 <package>https://cran.rstudio.com/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
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113 <package>https://cran.rstudio.com/src/contrib/plyr_1.8.4.tar.gz</package>
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92
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114 <package>https://cran.r-project.org/src/contrib/assertthat_0.2.0.tar.gz</package>
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115 <package>https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz</package>
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116 <package>https://cran.r-project.org/src/contrib/tibble_1.3.0.tar.gz</package>
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117 <package>https://cran.rstudio.com/src/contrib/dplyr_0.5.0.tar.gz</package>
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118 <package>https://cran.rstudio.com/src/contrib/tidyr_0.6.2.tar.gz</package>
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119 <package>https://cran.rstudio.com/src/contrib/reshape2_1.4.2.tar.gz</package>
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120 <package>https://cran.r-project.org/src/contrib/Archive/proto/proto_0.3-10.tar.gz</package>
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121 <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package>
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122 <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package>
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123 <package>https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz</package>
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124 <package>https://cran.r-project.org/src/contrib/Archive/doParallel/doParallel_1.0.8.tar.gz</package>
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125 <package>https://cran.r-project.org/src/contrib/Archive/colorspace/colorspace_1.2-4.tar.gz</package>
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95
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126 <package>https://cran.r-project.org/src/contrib/Archive/munsell/munsell_0.4.tar.gz</package>
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127 <package>https://cran.r-project.org/src/contrib/Archive/scales/scales_0.2.4.tar.gz</package>
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128 <package>https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz</package>
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129 <package>https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz</package>
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130 <package>https://cran.r-project.org/src/contrib/Archive/NMF/NMF_0.20.5.tar.gz</package>
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131 <package>https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz</package>
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132 <package>https://cran.rstudio.com/src/contrib/igraph_1.0.1.tar.gz</package>
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133 <package>https://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz</package>
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134 <package>https://cran.r-project.org/src/contrib/Archive/rstudioapi/rstudioapi_0.2.tar.gz</package>
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135 <package>https://cran.r-project.org/src/contrib/Archive/devtools/devtools_1.6.tar.gz</package>
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136 <package>https://cran.rstudio.com/src/contrib/mixOmics_6.1.2.tar.gz</package>
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137 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/bumphunter_1.10.0.tar.gz</package>
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138 <package>http://bioconductor.org/packages/3.2/bioc/src/contrib/minfi_1.16.1.tar.gz</package>
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4
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139 </action>
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140 </actions>
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141 </install>
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142 <readme>
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143 </readme>
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144 </package>
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145 </tool_dependency>
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