EpiRhandbook の bookdown 実行のスクラップ

$ sudo apt update &&\
  sudo apt install -y \
    cmake \
    build-essential \
    libxml2-dev \
    libudunits2-dev \
    libgdal-dev \
    libgeos-dev \
    libproj-dev \
    libglpk-dev \
    libsodium-dev \
    gdal-bin \
    gdal-data \
    pktools-dev \
    libmagick++-dev

$ sudo apt install openjdk-18-jdk
$ # openjdk-18 を指定する場合
$ # sudo R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-18-openjdk-amd64/ -e
$ R CMD javareconf -e
# 起動したシェルで R を起動
$ R

> # 起動した R session 内でパッケージのインストールを実行
> source("install_packages.R")
> q() # 一旦セッションを終了する

> bookdown::render_book(input = '.', output_format = 'bookdown::bs4_book', clean = TRUE, config_file = '_bookdown.yml')

> bookdown::render_book(input = '.', output_format = 'bookdown::bs4_book', clean = TRUE, config_file = '_small_bookdown.yml')

$ cp -a ./images/RStudio_overview.PNG ./images/RStudio_overview.png
$ cp -a ./images/markdown/8_ppttemplate.PNG ./images/markdown/8_ppttemplate.png
$ cp -a './images/Epi R Handbook Banner Beige 1500x500.png' ./images/Epi_R_Handbook_Banner_Beige_1500x500.png 
$ cp -a './images/Epi interview image.jpg' ./images/Epi_interview_image.jpg 
$ cp -a './images/Epi R Handbook Banner Japanese 1500x500.png' ./images/Epi_R_Handbook_Banner_Japanese_1500x500.png

$ docker run -it --rm --mount type=bind,source="$(pwd)",target=/opt/epiRhandbook_jp rocker/rstudio:4.3.2 /bin/bash
# 別シェルを立ち上げて変更をコミット
# docker commit <image id> <repository:tag>
# docker push <repository:tag>
$ docker commit <image id> ysaito8015/epirhandbook_jp:versionTag
$ docker push ysaito8015/epirhandbook_jp:versionTag

$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.3 LTS"

$ apt update &&\
  apt dist-upgrade -y &&\
  apt install -y \
    cmake \
    build-essential \
    pandoc \
    libxml2-dev \
    libudunits2-dev \
    libgdal-dev \
    libgeos-dev \
    libproj-dev \
    libglpk-dev \
    libsodium-dev \
    gdal-bin \
    gdal-data \
    pktools-dev \
    libmagick++-dev \
    openjdk-18-jdk \
    libharfbuzz-dev \
    libfribidi-dev
$ R CMD javareconf -e

# R パッケージのインストールを済ませておく
$ Rscript install_packages.R 2>&1 | tee ./log/install_packages.log

bookdown::render_book(
  input = '.',
  output_format = 'bookdown::bs4_book',
  clean = TRUE,
  config_file = '_bookdown.yml'
)

$ Rscript bookdown_build.R 2>&1 | tee ./log/bookdown_build.log

Warning messages:                                                                                                                           
1: In utils::install.packages(pkg_download[!installed_packages]) :                                                                          
  installation of package ‘ClassDiscovery’ had non-zero exit status                                                                         
2: In utils::install.packages(pkg_download[!installed_packages]) :                                                                          
  installation of package ‘PCDimension’ had non-zero exit status 

> pacman::p_load("ClassDiscovery")                                                                                                          
Installing package into ‘/usr/local/lib/R/site-library’                                                                                     
(as ‘lib’ is unspecified)                                                                                                                   
Warning: dependency ‘Biobase’ is not available                                                                                              
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest/src/contrib/ClassDiscovery_3.4.0.tar.gz'
Content type 'binary/octet-stream' length 506131 bytes (494 KB)
==================================================
downloaded 494 KB

ERROR: dependency ‘Biobase’ is not available for package ‘ClassDiscovery’
* removing ‘/usr/local/lib/R/site-library/ClassDiscovery’

The downloaded source packages are in
        ‘/tmp/RtmpVbROUE/downloaded_packages’
Warning messages:
1: In utils::install.packages(package, ...) :
  installation of package ‘ClassDiscovery’ had non-zero exit status

> BiocManager::install("Biobase", update = TRUE, ask = FALSE)

> BiocManager::install("ClassDiscovery", update = TRUE, ask = FALSE, force = TRUE)

> pacman::p_load("PCDimension")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest/src/contrib/PCDimension_1.1.13.tar.gz'
Content type 'binary/octet-stream' length 197878 bytes (193 KB)
==================================================
downloaded 193 KB

* installing *source* package ‘PCDimension’ ...
** package ‘PCDimension’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PCDimension)

The downloaded source packages are in
        ‘/tmp/RtmpVbROUE/downloaded_packages’

PCDimension installed

Failed with error:  ‘lazy-load database '/usr/local/lib/R/site-library/flextable/R/flextable.rdb' is corrupt’
In addition: Warning messages:
1: In FUN(X[[i]], ...) : restarting interrupted promise evaluation
2: In FUN(X[[i]], ...) : internal error -3 in R_decompress1

Warning message:
In pacman::p_load(bookdown, downlit, xml2, here, dplyr, incidence2,  :
  Failed to install/load:
downlit

> install.packages(c("renv", "yaml"))

> renv::restore()

> update.packages(ask = FALSE)

> bookdown::render_book(
  input = '.',
  output_format = 'bookdown::bs4_book',
  clean = TRUE,
  config_file = '_bookdown.yml'
)

> read_ncdf(file_paths[1])
no 'var' specified, using t2m, tp
other available variables:
 longitude, latitude, time
Will return stars object with 8760 cells.
No projection information found in nc file. 
 Coordinate variable units found to be degrees, 
 assuming WGS84 Lat/Lon.
stars object with 3 dimensions and 2 attributes
attribute(s):
           Min.  1st Qu.       Median         Mean      3rd Qu.         Max.
t2m [K] 256.459 276.7418 2.816750e+02 2.818962e+02 2.874753e+02 3.049785e+02
tp [m]    0.000   0.0000 2.328388e-06 1.137138e-04 5.704550e-05 8.477014e-03
dimension(s):
          from   to         offset   delta  refsys point values x/y
longitude    1    1             NA      NA  WGS 84    NA 10.423 [x]
latitude     1    1             NA      NA  WGS 84    NA 51.334 [y]
time         1 8760 2002-01-01 UTC 1 hours POSIXct    NA   NULL   


> read_ncdf(file_paths[2])
no 'var' specified, using t2m, tp
other available variables:
 longitude, latitude, time
Will return stars object with 8760 cells.
No projection information found in nc file. 
 Coordinate variable units found to be degrees, 
 assuming WGS84 Lat/Lon.
stars object with 3 dimensions and 2 attributes
attribute(s):
            Min.  1st Qu.       Median         Mean      3rd Qu.         Max.
t2m [K] 258.7856 275.4088 2.813136e+02 2.819685e+02 2.883852e+02 3.076843e+02
tp [m]    0.0000   0.0000 1.273918e-07 6.300391e-05 2.181585e-05 4.174184e-03
dimension(s):
          from   to         offset   delta  refsys point values x/y
longitude    1    1             NA      NA  WGS 84    NA 10.423 [x]
latitude     1    1             NA      NA  WGS 84    NA 51.334 [y]
time         1 8760 2003-01-01 UTC 1 hours POSIXct    NA   NULL    

 
> (read_ncdf(file_paths[1]) + read_ncdf(file_paths[2]))
no 'var' specified, using t2m, tp
other available variables:
 longitude, latitude, time
Will return stars object with 8760 cells.
No projection information found in nc file. 
 Coordinate variable units found to be degrees, 
 assuming WGS84 Lat/Lon.
no 'var' specified, using t2m, tp
other available variables:
 longitude, latitude, time
Will return stars object with 8760 cells.
No projection information found in nc file. 
 Coordinate variable units found to be degrees, 
 assuming WGS84 Lat/Lon.
Error in Ops.stars(read_ncdf(file_paths[1]), read_ncdf(file_paths[2])) : 
  (first) dimensions of e1 and e2 do not match

> a <- stars::read_ncdf(file_paths[1]) 
no 'var' specified, using t2m, tp
other available variables:
 longitude, latitude, time
Will return stars object with 8760 cells.
No projection information found in nc file. 
 Coordinate variable units found to be degrees, 
 assuming WGS84 Lat/Lon.
> b <- stars::read_ncdf(file_paths[2])
no 'var' specified, using t2m, tp
other available variables:
 longitude, latitude, time
Will return stars object with 8760 cells.
No projection information found in nc file. 
 Coordinate variable units found to be degrees, 
 assuming WGS84 Lat/Lon.
> dim(a)
longitude  latitude      time 
        1         1      8760 
> dim(b)
longitude  latitude      time 
        1         1      8760 

data <- stars::read_stars(file_paths)

pacman::p_load(doParallel)
makePSOCKcluster(1)

> sitrep::find_end_date()
> sitrep::find_start_date()

label: observation_time                                               
Quitting from lines 19167-19211 (_main.Rmd) 
Error: object 'add_weights_cluster' is not exported by 'namespace:epikit'
In addition: There were 50 or more warnings (use warnings() to see the first 50)

> knitr::knit2html(input="./new_pages/survival_analysis.Rmd") 

label: observation_time
Quitting from lines 19166-19210 (_main.Rmd) 
Error in find_end_date(., "left_date", "death_date", period_start = "recall_start",  : 
  could not find function "find_end_date"
In addition: There were 50 or more warnings (use warnings() to see the first 50)

> install.packages("drat", repos = "https://cran.rstudio.com")
> drat::addRepo("R4EPI")
> install.packages("sitrep")

$ apt update && \
  apt install -y  libudunits2-dev libgdal-dev libgeos-dev libproj-dev

$ apt update && apt install -y libglpk-dev

> # 緯度経度の範囲に基図を切り取る。タイル種別を選択。
> map <- OpenStreetMap::openmap(
+   upperLeft = c(max(linelist$lat, na.rm=T), max(linelist$lon, na.rm=T)),   # 基図のタイルの制限
+   lowerRight = c(min(linelist$lat, na.rm=T), min(linelist$lon, na.rm=T)),
+   zoom = NULL,
+   type = c("osm", "stamen-toner", "stamen-terrain", "stamen-watercolor", "esri","esri-topo")[1])
Error:  .onLoad は loadNamespace()（'rJava' に対する）の中で失敗しました、詳細は: 
  call: fun(libname, pkgname) 
  error: JAVA_HOME cannot be determined from the Registry 

label: unnamed-chunk-943
Quitting from lines 20951-20955 (_main.Rmd) 
Error: A data frame is not a valid object for this function.
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Registered S3 method overwritten by 'ape':
  method   from 
  plot.mst spdep

dplyr::filter(sle_adm3_raw, "admin2Name" %in% c("Western Area Urban", "Western Area Rural")) 

label: clean_adm3 (with options) 
List of 1
 $ message: logi FALSE

Quitting from lines 20966-20971 (_main.Rmd) 
Error in UseMethod("filter") : 
  no applicable method for 'filter' applied to an object of class "logical"
In addition: There were 50 or more warnings (use warnings() to see the first 50)

## パッケージのインストールとロード
pacman::p_load(tidyverse, EpiNow2, EpiEstim, here, incidence2, epicontacts, rio, projections)

## ラインリストのロード
linelist <- import(here::here("data", "case_linelists", "linelist_cleaned.rds"))

## コンタクトの作成
contacts <- linelist %>%
  transmute(
    from = infector,
    to = case_id
  ) %>%
  drop_na()

## エピコンタクトの作成
epic <- make_epicontacts(
  linelist = linelist,
  contacts = contacts, 
  directed = TRUE
)

## ## estimate gamma generation time
## generation_time <- bootstrapped_dist_fit(
##   get_pairwise(epic, "date_infection"),
##   dist = "gamma",
##   max_value = 20,
##   bootstraps = 1
## )

## ## export for caching
## export(
##   generation_time,
##   here("data/cache/epidemic_models/generation_time.rds")
## )

## import cached generation time
generation_time <- import(here("data/cache/epidemic_models/generation_time.rds"))

## ## estimate incubation period
## incubation_period <- bootstrapped_dist_fit(
##   linelist$date_onset - linelist$date_infection,
##   dist = "lognormal",
##   max_value = 100,
##   bootstraps = 1
## )

## ## export for caching
## export(
##   incubation_period,
##   here("data/cache/epidemic_models/incubation_period.rds")
## )

## import cached incubation period
incubation_period <- import(here("data/cache/epidemic_models/incubation_period.rds"))

## get incidence from onset date
cases <- linelist %>%
  group_by(date = date_onset) %>%
  summarise(confirm = n())

## ## run epinow
## epinow_res <- epinow(
##   reported_cases = cases,
##   generation_time = generation_time,
##   delays = delay_opts(incubation_period),
##   target_folder = here("data/cache/epidemic_models"),
##   return_output = TRUE,
##   output = "samples",
##   verbose = TRUE,
##   stan = stan_opts(samples = 750, chains = 4),
##   horizon = 21
## )

## ## export for caching
## export(
##   epinow_res,
##   here("data/cache/epidemic_models/epinow_res.rds")
## )

## import cached epinow results
epinow_res <- import(here("data/cache/epidemic_models/epinow_res.rds"))

## plot summary figure
plot(epinow_res)

> remotes::install_github("reconhub/epicontacts@timeline")

Error: package or namespace load failed for ‘ igraph’  in dyn.load(file, DLLpath = DLLpath, ...):                                                 
 unable to load shared object '/home/ysaito/.asdf/installs/R/4.2.1/lib/R/library/00LOCK-igraph/00new/igraph/libs/igraph.so':                      
  libgfortran.so.4: cannot open shared object file: No such file or directory                                                                     
Error: loading failed                                                                                                                             
Execution halted                                                                                                                                  
ERROR: loading failed                                                                                                                             
* removing ‘ /home/ysaito/.asdf/installs/R/4.2.1/lib/R/library/igraph’                                                                            
* restoring previous ‘ /home/ysaito/.asdf/installs/R/4.2.1/lib/R/library/igraph’                                                                  
                                                                                                                                                  
The downloaded source packages are in                                                                                                             
        ‘ /tmp/RtmpYOE39D/downloaded_packages’                                                                                                    
Updating HTML index of packages in '.Library'                                                                                                     
Making 'packages.html' ... done                                                                                                                   
Warning message:                                                                                                                                  
In install.packages("igraph") :                                                                                                                   
  installation of package ‘ igraph’  had non-zero exit status 

$ apt install gfortran-7

> update.packages(ask = FALSE)
> remotes::install_github("reconhub/epicontacts@timeline", force = TRUE)

epic_small <- epic %>% 
  subset(
    node_attribute = list(date_onset = c(as.Date(c("2014-06-01", "2014-07-01"))))) %>%
  epicontacts::thin("contacts")

> BiocManager::install(update = TRUE, ask = FALSE)

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://packagemanager.rstudio.com/cran/__linux__/focal/latest

Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Old packages: 'ggtree'
Update all/some/none? [a/s/n]: a
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/ggtree_3.4.4.tar.gz'
Content type 'application/x-gzip' length 356386 bytes (348 KB)
==================================================
downloaded 348 KB

* installing *source* package ‘ggtree’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'warning_wrap' not found
Error: unable to load R code in package ‘ggtree’
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/usr/local/lib/R/site-library/ggtree’
* restoring previous ‘/usr/local/lib/R/site-library/ggtree’

The downloaded source packages are in
        ‘/tmp/RtmpHOCJiG/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘ggtree’ had non-zero exit status

>  remotes::install_github('YuLab-SMU/ggtree')

Quitting from lines 11228-11251 [unnamed-chunk-599] (_main.Rmd)                                                                                   
Error:                                                                                                                                            
! object 'gender' not found                                                                                                                       
Backtrace:                                                                                                                                        
 1. incidence2::incidence(...)                                                                                                                    
Execution halted  

outbreak <- incidence2::incidence(   
     x = linelist,                   # データフレームを指定する（linelist全体）
     date_index = "date_onset",      # 日付の列
     interval = "week",              # 週ごとに集計
     groups = "gender")              # 性別によるグルーピング
     #na_as_group = TRUE)            # 性別の欠損値は欠損のグループ（NA）として扱う

Quitting from lines 30055-30058 [unnamed-chunk-1301] (_main.Rmd)
Error in `tree_subset()`:
! could not find function "tree_subset"
Execution halted
l

Quitting from lines 30071-30075 [unnamed-chunk-1303] (_main.Rmd)
Error in `tree_subset()`:
! could not find function "tree_subset"
Execution halted

sub_tree1 <- tidytree::tree_subset(
  tree,
  node = 528)