s20190616_installMonocle3.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)\n",
      "Update old packages: 'caret', 'dbplyr', 'devtools', 'digest', 'dplyr',\n",
      "  'evaluate', 'forecast', 'fs', 'ggplot2', 'gower', 'hexbin', 'htmlwidgets',\n",
      "  'ipred', 'IRkernel', 'knitr', 'lmtest', 'markdown', 'mime', 'nlme',\n",
      "  'numDeriv', 'openssl', 'pillar', 'progress', 'quadprog', 'quantmod',\n",
      "  'RcppArmadillo', 'repr', 'reprex', 'rmarkdown', 'rvest', 'shiny', 'sparklyr',\n",
      "  'tibble', 'tinytex', 'tseries', 'xfun', 'xts', 'zoo'\n",
      "Warning message:\n",
      "“package ‘methods’ is not available (for R version 3.5.1)”Warning message:\n",
      "“package ‘methods’ is a base package, and should not be updated”Downloading GitHub repo cole-trapnell-lab/monocle3@master\n",
      "from URL https://api.github.com/repos/cole-trapnell-lab/monocle3/zipball/master\n",
      "Installing monocle3\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/dplyr_0.8.1.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools134a7eca63'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/ggplot2_3.2.0.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools1333e79104'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/ggrepel_0.8.1.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools133e6fa05f'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/grr_0.9.5.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13618d6cd1'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/htmlwidgets_1.3.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools1396731cf'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/igraph_1.2.4.1.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools1349e7dbda'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/irlba_2.3.3.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools135f6888c7'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/lmtest_0.9-37.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools136a7576f3'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/Matrix.utils_0.9.7.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools1373129139'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/pbapply_1.4-0.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools133794544a'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/pbmcapply_1.4.1.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13755aa4a3'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/pheatmap_1.0.12.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13508b5aca'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/plotly_4.9.0.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools135ef98197'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/proxy_0.4-23.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools1332b3d23a'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/pryr_0.1.4.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools135660e6c7'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/pscl_1.5.2.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13555c2103'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/RANN_2.6.1.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools1355954cf7'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/RcppParallel_4.4.3.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools133acdaa45'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/reticulate_1.12.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13264431ef'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/RhpcBLASctl_0.18-205.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools136bcd4b75'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/Rtsne_0.15.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools133f6638f'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/shiny_1.3.2.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13298a1881'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/slam_0.1-45.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools139f3f5c1'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/spdep_1.1-2.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13e40f527'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/speedglm_0.3-2.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools132e1e8dfa'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/tibble_2.1.3.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13385a91'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/uwot_0.1.3.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13118bacf7'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Warning message in system(cmd):\n",
      "“error in running command”Warning message in utils::untar(src, exdir = target, compressed = \"gzip\"):\n",
      "“‘/bin/gtar -xf '/tmp/Rtmp7Rj2or/viridis_0.5.1.tar.gz' -C '/tmp/Rtmp7Rj2or/devtools13104651eb'’ returned error code 127”Warning message in system(paste(TAR, \"--version >\", tf, \"2>&1\")):\n",
      "“error in running command”Installation failed: error in running command\n",
      "'/opt/conda/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \\\n",
      "  --quiet CMD INSTALL  \\\n",
      "  '/tmp/Rtmp7Rj2or/devtools134f78f5ff/cole-trapnell-lab-monocle3-7427951'  \\\n",
      "  --library='/opt/conda/lib/R/library' --install-tests \n",
      "\n",
      "Installation failed: Command failed (1)\n"
     ]
    }
   ],
   "source": [
    "if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n",
    "    install.packages(\"BiocManager\")\n",
    "BiocManager::install()\n",
    "\n",
    "#options(unzip = \"internal\")\n",
    "install.packages('methods',dependencies=TRUE, repos='cran.rstudio.com/')\n",
    "\n",
    "devtools::install_github('cole-trapnell-lab/monocle3')"
   ]
  }
 ],
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