tested dependencies and scripts for ubuntu18.04

mxochicale-phd · Sep 1, 2019 · d3c304e · d3c304e
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diff --git a/0_code_data/0_data/readme.md b/0_code_data/0_data/readme.md
@@ -0,0 +1,76 @@
+
+
+```
+$HOME/phd/thesis/0_code_data/0_data$ tree -s
+.
+├── [       4096]  0_raw-timeseries
+│   ├── [       4096]  hii
+│   │   ├── [   28185223]  hii-HS01-TidiedInterpolatedRawData.dt
+│   │   ├── [   31486666]  hii-HS02-TidiedInterpolatedRawData.dt
+│   │   ├── [   28817382]  hii-HS03-TidiedInterpolatedRawData.dt
+│   │   └── [   33532170]  hii-HS04-TidiedInterpolatedRawData.dt
+│   └── [       4096]  hri
+│       └── [   39876955]  hri-TidiedInterpolatedRawData.dt
+└── [       4096]  1_datasets
+    ├── [       4096]  hii
+    │   ├── [       4096]  3Drqa
+    │   │   ├── [     562935]  RQAs_p01w100_H_HS01_HNnb.dt
+    │   │   ├── [     609120]  RQAs_p01w250_H_HS01_HNnb.dt
+    │   │   ├── [     614775]  RQAs_p01w500_H.dt
+    │   │   ├── [    2453610]  RQAs_p01w500_H_HS01.dt
+    │   │   ├── [     614775]  RQAs_p01w500_H_HS01_HNnb.dt
+    │   │   ├── [    2453275]  RQAs_p01w500_H_HS02.dt
+    │   │   ├── [     614775]  RQAs_p01w500_HS01_HNnb.dt
+    │   │   ├── [     614775]  RQAs_p01w500_HS01_HNnb_sg0.dt
+    │   │   ├── [     615248]  RQAs_p01w500_HS01_HNnb_sg1.dt
+    │   │   ├── [     582483]  RQAs_p01w500_HS01_HNnb_sg2.dt
+    │   │   ├── [    2454576]  RQAs_p01w500_V_HS01.dt
+    │   │   ├── [    2450780]  RQAs_p01w500_V_HS02.dt
+    │   │   ├── [     620034]  RQAs_p01w750_H_HS01_HNnb.dt
+    │   │   ├── [     620181]  RQAs_p04w500_HS01_HNnb.dt
+    │   │   ├── [     619994]  RQAs_p05w500_HS01_HNnb.dt
+    │   │   └── [     616640]  RQAs_p10w500_HS01_HNnb.dt
+    │   ├── [       4096]  dataset
+    │   │   └── [   24798863]  xdata.dt
+    │   ├── [       4096]  rqa
+    │   │   └── [     111776]  rqa_w10.dt
+    │   └── [       4096]  utde
+    │       ├── [       5376]  aMED-H-w10.dt
+    │       ├── [       5376]  aMED-V-w10.dt
+    │       ├── [    3642508]  AMI-w10.dt
+    │       ├── [    3874152]  EE-w10.dt
+    │       ├── [     225275]  MED-w10.dt
+    │       └── [      24336]  MTD-w10.dt
+    └── [       4096]  hri
+        ├── [       4096]  3Drqa
+        │   ├── [     563401]  RQAs_p01w100_HS01_HN_w100.dt
+        │   ├── [     612207]  RQAs_p01w250_HS01_HN_w250.dt
+        │   ├── [     615278]  RQAs_p01w500_H.dt
+        │   ├── [    1225100]  RQAs_p01w500_HS01_HNHF.dt
+        │   ├── [     615278]  RQAs_p01w500_HS01_HN_w500.dt
+        │   ├── [     615278]  RQAs_p01w500_HS01_HN_w500_sg0.dt
+        │   ├── [     612301]  RQAs_p01w500_HS01_HN_w500_sg1.dt
+        │   ├── [     566502]  RQAs_p01w500_HS01_HN_w500_sg2.dt
+        │   ├── [    1228884]  RQAs_p01w500_HS01_VNVF.dt
+        │   ├── [    2297987]  RQAs_p01w500_HV.dt
+        │   ├── [    1228740]  RQAs_p01w500_RS01_HNHF.dt
+        │   ├── [    1217725]  RQAs_p01w500_RS01_VNVF.dt
+        │   ├── [     619826]  RQAs_p01w750_HS01_HN_w750.dt
+        │   ├── [     553538]  RQAs_p02w500_H.dt
+        │   ├── [     615577]  RQAs_p03w500_H.dt
+        │   └── [     615862]  RQAs_p04w500_H.dt
+        ├── [       4096]  dataset
+        │   └── [   45532251]  xdata.dt
+        ├── [       4096]  rqa
+        │   └── [     179635]  rqa_w10.dt
+        └── [       4096]  utde
+            ├── [       8448]  aMED-H-w10.dt
+            ├── [       8448]  aMED-V-w10.dt
+            ├── [    5119480]  AMI-w10.dt
+            ├── [    6283402]  EE-w10.dt
+            ├── [     356219]  MED-w10.dt
+            └── [      33856]  MTD-w10.dt
+
+14 directories, 53 files
+
+```
diff --git a/0_code_data/1_code/0_machineinfo/machineinfo.sh b/0_code_data/1_code/0_machineinfo/machineinfo.sh
@@ -1,5 +1,8 @@
 clear
 
+echo '#################################################################'
+echo '## Date'
+date
 
 echo '#################################################################'
 echo '## Ubuntu Version: $lsb_release -a'

diff --git a/0_code_data/1_code/0_machineinfo/output-ubuntu1804.md b/0_code_data/1_code/0_machineinfo/output-ubuntu1804.md
@@ -1,11 +1,9 @@
 
 ```
-sh machineinfo.sh
-```
-on Sun 11 Aug 17:34:52 BST 2019
-
-
-```
+xima@blue:~/phd/thesis/0_code_data/1_code/0_machineinfo$ sh machineinfo.sh 
+#################################################################
+## Date
+Fri 30 Aug 21:42:13 BST 2019
 #################################################################
 ## Ubuntu Version: $lsb_release -a
 No LSB modules are available.
@@ -25,7 +23,7 @@ vendor_id	: GenuineIntel
 #GRAPHIC CARD INFO:  $lspci -vnn | grep VGA -A 12
 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07) (prog-if 00 [VGA controller])
 	Subsystem: Huawei Technologies Co., Ltd. UHD Graphics 620 [19e5:3e04]
-	Flags: bus master, fast devsel, latency 0, IRQ 139
+	Flags: bus master, fast devsel, latency 0, IRQ 138
 	Memory at 2ff2000000 (64-bit, non-prefetchable) [size=16M]
 	Memory at 2fc0000000 (64-bit, prefetchable) [size=256M]
 	I/O ports at 3000 [size=64]
@@ -36,7 +34,8 @@ vendor_id	: GenuineIntel
 
 00:04.0 Signal processing controller [1180]: Intel Corporation Xeon E3-1200 v5/E3-1500 v5/6th Gen Core Processor Thermal Subsystem [8086:1903] (rev 08)
 	Subsystem: Huawei Technologies Co., Ltd. Xeon E3-1200 v5/E3-1500 v5/6th Gen Core Processor Thermal Subsystem [19e5:3e04]
-xima@blue:~/phd/thesis/0_code_data/1_code/0_machineinfo$ 
+
+
 ```
 
 
diff --git a/0_code_data/1_code/1_dependencies/A_install-R.sh b/0_code_data/1_code/1_dependencies/A_install-R.sh
@@ -1,48 +1,98 @@
 #!/bin/bash  
 
-##USAGE:
-#chmod +x file
-#./file
+# references
+## MAIN REFERENCE: https://cloud.r-project.org/bin/linux/ubuntu/README.html
+## https://gist.github.com/ElToro1966/999f1c8ca51a75648dd587a3170e4335
 
+# key
+sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 
 
-sudo apt-key adv –keyserver keyserver.ubuntu.com –recv-keys E084DAB9
-##or
-#gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
-#gpg -a --export E084DAB9 | sudo apt-key add -
-
-
-
-#SELECT UBUNTU VERSION
-
-# Basic format of next line deb https://<my.favorite.cran.mirror>/bin/linux/ubuntu <enter your ubuntu version>/
-#sudo add-apt-repository 'deb https://cran.ma.imperial.ac.uk/bin/linux/ubuntu precise/'
-
-## Ubuntu 12.04: precise
-#sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu precise/'
-
-## Ubuntu 14.04: trusty
-sudo add-apt-repository 'deb-src https://cloud.r-project.org/bin/linux/ubuntu trusty/'
-
-### Ubuntu 16.04: xenial
-#sudo add-apt-repository 'deb-src https://cloud.r-project.org/bin/linux/ubuntu xenial'
-
-
+## Ubuntu 18.04: bionic
+sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
 
 sudo apt-get update
 
 
 ## DEPENDENCIES
 sudo apt-get update
 sudo apt-get --yes install gfortran
-sudo apt-get --yes install libblas-dev libatlas-base-dev liblapack-dev libatlas-base-dev libncurses5-dev
-sudo apt-get --yes install cdbs
-sudo apt-get --yes install r-base r-base-dev
+sudo apt-get --yes install libblas-dev libatlas-base-dev liblapack-dev libatlas-base-dev libncurses5-dev libopenblas-dev 
+sudo apt-get --yes install cdbs gdebi 
+
+
+sudo apt-get --yes install xorg  #X11
+sudo apt-get --yes install libx11-dev  #X11
+sudo apt-get --yes install libglu1-mesa-dev #X11
+#ref https://stackoverflow.com/questions/31820865/installing-rgl-on-ubuntu-and-mac-x11-not-found 
+
+sudo apt-get --yes install libfreetype6 libfreetype6-dev # 'freetype2'
+#ref https://github.com/jwilm/alacritty/issues/1623
 
 
 ## devtools dependencies
 sudo apt-get --yes install libssl-dev libcurl4-openssl-dev
 sudo apt-get --yes install libxml2-dev # for xml2 calling load_all()
 sudo apt-get --yes install r-cran-rgl # rgl for nonlinearTseries
 
+## r-base r-base-dev  
+sudo apt-get --yes install r-base r-base-dev
+
+
+
+
+
 
+########################################
+########################################
+## For the following versions of Ubuntu
+## 12.04, 14.04, 16.04
+#
+##!/bin/bash  
+#
+###USAGE:
+##chmod +x file
+##./file
+#
+#
+#
+#sudo apt-key adv –keyserver keyserver.ubuntu.com –recv-keys E084DAB9
+###or
+##gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
+##gpg -a --export E084DAB9 | sudo apt-key add -
+#
+#
+#
+##SELECT UBUNTU VERSION
+#
+## Basic format of next line deb https://<my.favorite.cran.mirror>/bin/linux/ubuntu <enter your ubuntu version>/
+##sudo add-apt-repository 'deb https://cran.ma.imperial.ac.uk/bin/linux/ubuntu precise/'
+#
+### Ubuntu 12.04: precise
+##sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu precise/'
+#
+### Ubuntu 14.04: trusty
+#sudo add-apt-repository 'deb-src https://cloud.r-project.org/bin/linux/ubuntu trusty/'
+#
+#### Ubuntu 16.04: xenial
+##sudo add-apt-repository 'deb-src https://cloud.r-project.org/bin/linux/ubuntu xenial'
+#
+#
+#
+#sudo apt-get update
+#
+#
+### DEPENDENCIES
+#sudo apt-get update
+#sudo apt-get --yes install gfortran
+#sudo apt-get --yes install libblas-dev libatlas-base-dev liblapack-dev libatlas-base-dev libncurses5-dev
+#sudo apt-get --yes install cdbs
+#sudo apt-get --yes install r-base r-base-dev
+#
+#
+### devtools dependencies
+#sudo apt-get --yes install libssl-dev libcurl4-openssl-dev
+#sudo apt-get --yes install libxml2-dev # for xml2 calling load_all()
+#sudo apt-get --yes install r-cran-rgl # rgl for nonlinearTseries
+#
+#
diff --git a/0_code_data/1_code/1_dependencies/B_install-basic-packages.R b/0_code_data/1_code/1_dependencies/B_install-basic-packages.R
@@ -1,18 +1,18 @@
 
 mirror_repo <- 'https://www.stats.bris.ac.uk/R/'
 
-## OTHER UK MIRRORS
-#  https://www.stats.bris.ac.uk/R/
-#  http://www.stats.bris.ac.uk/R/
-#  https://mirrors.ebi.ac.uk/CRAN/
-#  http://mirrors.ebi.ac.uk/CRAN/
-#  https://cran.ma.imperial.ac.uk/
-#  http://cran.ma.imperial.ac.uk/
-#  http://mirror.mdx.ac.uk/R/
-
-
-
-### devtools
+####################
+## OTHER POTENTIAL UK MIRRORS (NOT TESTED)
+# http://www.stats.bris.ac.uk/R/
+# https://mirrors.ebi.ac.uk/CRAN/
+# http://mirrors.ebi.ac.uk/CRAN/
+# https://cran.ma.imperial.ac.uk/
+# http://cran.ma.imperial.ac.uk/
+# http://mirror.mdx.ac.uk/R/
+# https://www.stats.bris.ac.uk/R/
+
+
+#### devtools
 install.packages("devtools", repos=mirror_repo, dependencies = TRUE)
 
 #### [data.table]([https://github.com/Rdatatable/data.table/wiki/Installation)

diff --git a/0_code_data/1_code/1_dependencies/D_install-octave.sh b/0_code_data/1_code/1_dependencies/D_install-octave.sh
@@ -1,6 +1,6 @@
 #!/bin/bash  
 
-
+# download and installation
 cd ~/Downloads
 wget ftp://ftp.gnu.org/gnu/octave/octave-4.0.2.tar.gz
 tar xf octave-4.0.2.tar.gz
@@ -9,10 +9,48 @@ cd octave-4.0.2/
 make 
 sudo make install
 
-# remove
+# remove installation path and tar file
 rm -rf octave-4.0.2
 rm octave-4.0.2.tar.gz 
 
 
 
+#
+#remove octave [:link:](https://askubuntu.com/questions/814054/uninstalling-octave-from-ubuntu-16-04-lts)
+#```
+#sudo make uninstall
+#
+#```
+#
+#
+#
+#References: 
+#* GNU Octave, version 4.0.2 [:link:](https://unix.stackexchange.com/questions/280195/how-to-install-octave-without-gui-in-ubuntu-16-0://unix.stackexchange.com/questions/280195/how-to-install-octave-without-gui-in-ubuntu-16-04)
+#
+#* withouht: sudo apt-get build-dep octave [:link:](https://askubuntu.com/questions/730322/how-to-install-octave-in-ubuntu-14-04-using-terminal#comment1083602_730333)
+#
+#
+#
+### ISSUES
+#
+#### GNU Octave 4.2.2 Installation in Ubuntu 16.04
+#*(this versions has an issue with undefined variables when calling functions )*
+#
+#```
+#sudo add-apt-repository ppa:octave/stable
+#sudo apt-get update
+#sudo apt-get install octave octave-signal octave-control
+#```
+#remove octave [:link:](https://askubuntu.com/questions/814054/uninstalling-octave-from-ubuntu-16-04-lts) 
+#```
+#sudo apt-get remove --auto-remove octave
+#```
+#
+#
+# UBUNTU 18.04
+#
+#sudo apt-get install octave
+#sudo apt-get remove --auto-remove octave
+#
+