Merge pull request #36 from covidclinical/topic-install-stm

Topic install stm

Author: nathan-palmer

Dockerfile

@@ -273,6 +273,9 @@ RUN cp /usr/include/oracle/${ORACLE_RELEASE}.${ORACLE_UPDATE}/client64/* $ORACLE
 # install ROracle
 RUN Rscript -e "install.packages('ROracle')" 
 
+# we're going to move to using the remotes package to makage package installation going forward
+RUN Rscript --vanilla -e "remotes::install_cran('stm', repos='https://cran.microsoft.com/snapshot/2021-11-18')"
+
  # allow modification of these locations so users can install R packages without warnings
 RUN chmod -R 777 /opt/microsoft/ropen/$MRO_VERSION/lib64/R/library
 RUN chmod -R 777 /opt/microsoft/ropen/$MRO_VERSION/lib64/R/doc/html/packages.html
@@ -285,8 +288,8 @@ RUN chmod -R 777 /opt/microsoft/ropen/$MRO_VERSION/lib64/R/doc/html/packages.htm
 RUN mkdir /opt/rstudioserver
 WORKDIR /opt/rstudioserver
 
-RUN wget http://archive.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb
-RUN dpkg -i ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb
+RUN wget http://archive.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb
+RUN dpkg -i ./libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb
 
 RUN apt-get update && apt-get install -y gdebi-core
 

README.md

@@ -37,7 +37,7 @@ docker run --rm --name 4ce -d -v /SOME_LOCAL_PATH:/4ceData \
                             -p 2200:22 \
                             -e CONTAINER_USER_USERNAME=REPLACE_ME_USERNAME \
                             -e CONTAINER_USER_PASSWORD=REPLACE_ME_PASSWORD \
-                            dbmi/4ce-analysis:version-2.3.0
+                            dbmi/4ce-analysis:version-2.4.0
 ```
 
 *Previous versions of this documentation suggested running the ``latest`` tag of the image. For reproducibility, we are now asking
@@ -65,8 +65,8 @@ The ``-p`` flag to Docker maps a TCP port in the container to a TCP port on the
 
 ### Image Name and Tag (Version)
 
-The final line of the Docker command above: ``dbmi/4ce-analysis:version-2.3.0`` specifies the image name and tag that will be run.
-The image name is ``dbmi/4ce-analysis`` and the tag is the string following the colon, e.g. ``version-2.3.0``. 
+The final line of the Docker command above: ``dbmi/4ce-analysis:version-2.4.0`` specifies the image name and tag that will be run.
+The image name is ``dbmi/4ce-analysis`` and the tag is the string following the colon, e.g. ``version-2.4.0``. 
 We will use tags to track the version of the container that each site is running locally.
 We will attempt to keep this documentation up-to-date with instructions for running the latest release version, but you can 
 always refer to the container's registry page https://hub.docker.com/repository/docker/dbmi/4ce-analysis/tags?page=1 for 
@@ -169,7 +169,7 @@ connect to the container.
 A final option is to run the container in a way that directly presents the user with an interactive R session. The container will stop after you quit this R session. Note, this command runs the container so you can't already have one running when issuing it. The --rm flag will ensure that when the R session is quit, the container is stopped and cleaned up.
 
 ```bash
-docker run --name 4ce -v /SOME_LOCAL_PATH:/4ceData --rm -it dbmi/4ce-analysis:version-2.3.0 R
+docker run --name 4ce -v /SOME_LOCAL_PATH:/4ceData --rm -it dbmi/4ce-analysis:version-2.4.0 R
 ```
 
 
@@ -183,7 +183,7 @@ In more detail, the steps are are follows:
 
 ### 1. On the *bastion* host: Pull the container image from the registry
 ```bash
-docker image rm dbmi/4ce-analysis:version-2.3.0
+docker image rm dbmi/4ce-analysis:version-2.4.0
 docker pull dbmi/4ce-analysis
 ```
 

R_VERSIONS

@@ -62,6 +62,7 @@ FactToCube 0.0.0.9000
 fansi 0.4.2
 farver 2.0.3
 fastmap 1.1.0
+fastmatch 1.1-3
 fmsb 0.7.0
 forcats 0.5.1
 foreach 1.5.1
@@ -103,6 +104,7 @@ icd.data 1.0
 ini 0.3.1
 ipred 0.9-9
 isoband 0.2.3
+ISOcodes 2021.02.24
 iterators 1.0.11
 jquerylib 0.1.3
 jsonlite 1.7.2
@@ -116,6 +118,7 @@ later 1.1.0.1
 lattice 0.20-41
 lava 1.6.8.1
 lazyeval 0.2.2
+lda 1.4.2
 lifecycle 0.2.0
 lme4 1.1-26
 lubridate 1.7.9.2
@@ -168,6 +171,7 @@ promises 1.1.1
 ps 1.5.0
 purrr 0.3.4
 quadprog 1.5-8
+quanteda 3.1.0
 quantreg 5.83
 R.methodsS3 1.8.1
 R.oo 1.24.0
@@ -178,6 +182,7 @@ RColorBrewer 1.1-2
 Rcpp 1.0.6
 RcppArmadillo 0.10.1.2.2
 RcppEigen 0.3.3.7.0
+RcppParallel 5.1.4
 readr 1.4.0
 readxl 1.3.1
 recipes 0.1.15
@@ -213,6 +218,8 @@ selectr 0.4-2
 sessioninfo 1.1.1
 shape 1.4.5
 shiny 1.6.0
+slam 0.1-49
+SnowballC 0.7.0
 sourcetools 0.1.7
 sp 1.4-5
 SparseM 1.78
@@ -222,6 +229,8 @@ SQUAREM 2021.1
 statmod 1.4.35
 stats 4.0.2
 stats4 4.0.2
+stm 1.3.6
+stopwords 2.3
 stringi 1.5.3
 stringr 1.4.0
 SurrogateTest 1.2

UBUNTU_VERSION

@@ -1,4 +1,4 @@
 Distributor ID:	Ubuntu
-Description:	Ubuntu 20.04.2 LTS
+Description:	Ubuntu 20.04.3 LTS
 Release:	20.04
 Codename:	focal