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OHDSI / DatabaseConnector

An R package for connecting to databases using JDBC.
http://ohdsi.github.io/DatabaseConnector/
54 stars 81 forks source link

Installation of `DatabaseConnector` on 🚩🇨🇳🏹红旗中科 RedFlag Linux (🍥Debian 11) #196

Closed englianhu closed 2 years ago

englianhu commented 2 years ago 
:~$ sudo su - -c "R -e \"install.packages(c('DatabaseConnector'), repos = 'https://cran.rstudio.com', lib = '/usr/lib/R/library', dependencies = TRUE, INSTALL_opts = '--no-lock')\""                         
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R是自由软件，不带任何担保。
在某些条件下你可以将其自由散布。
用'license()'或'licence()'来看散布的详细条件。

R是个合作计划，有许多人为之做出了贡献.
用'contributors()'来看合作者的详细情况
用'citation()'会告诉你如何在出版物中正确地引用R或R程序包。

用'demo()'来看一些示范程序，用'help()'来阅读在线帮助文件，或
用'help.start()'通过HTML浏览器来看帮助文件。
用'q()'退出R.

> install.packages(c('DatabaseConnector'), repos = 'https://cran.rstudio.com', lib = '/usr/lib/R/library', dependencies = TRUE, INSTALL_opts = '--no-lock')
还安装相依关系‘aws.signature’, ‘palmerpenguins’, ‘plogr’, ‘aws.s3’, ‘DBItest’, ‘RSQLite’, ‘ssh’, ‘Andromeda’

试开URL’https://cran.rstudio.com/src/contrib/aws.signature_0.6.0.tar.gz'
Content type 'application/x-gzip' length 28571 bytes (27 KB)
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downloaded 27 KB

试开URL’https://cran.rstudio.com/src/contrib/palmerpenguins_0.1.1.tar.gz'
Content type 'application/x-gzip' length 2995960 bytes (2.9 MB)
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downloaded 2.9 MB

试开URL’https://cran.rstudio.com/src/contrib/plogr_0.2.0.tar.gz'
Content type 'application/x-gzip' length 7795 bytes
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downloaded 7795 bytes

试开URL’https://cran.rstudio.com/src/contrib/aws.s3_0.3.21.tar.gz'
Content type 'application/x-gzip' length 54667 bytes (53 KB)
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downloaded 53 KB

试开URL’https://cran.rstudio.com/src/contrib/DBItest_1.7.2.tar.gz'
Content type 'application/x-gzip' length 102854 bytes (100 KB)
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downloaded 100 KB

试开URL’https://cran.rstudio.com/src/contrib/RSQLite_2.2.16.tar.gz'
Content type 'application/x-gzip' length 3704913 bytes (3.5 MB)
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downloaded 3.5 MB

试开URL’https://cran.rstudio.com/src/contrib/ssh_0.8.0.tar.gz'
Content type 'application/x-gzip' length 1110079 bytes (1.1 MB)
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downloaded 1.1 MB

试开URL’https://cran.rstudio.com/src/contrib/Andromeda_0.6.1.tar.gz'
Content type 'application/x-gzip' length 243882 bytes (238 KB)
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downloaded 238 KB

试开URL’https://cran.rstudio.com/src/contrib/DatabaseConnector_5.0.4.tar.gz'
Content type 'application/x-gzip' length 712654 bytes (695 KB)
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* installing *source* package ‘aws.signature’ ...
** 成功将‘aws.signature’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aws.signature)
* installing *source* package ‘palmerpenguins’ ...
** 成功将‘palmerpenguins’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (palmerpenguins)
* installing *source* package ‘plogr’ ...
** 成功将‘plogr’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (plogr)
* installing *source* package ‘ssh’ ...
** 成功将‘ssh’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
Package libssh was not found in the pkg-config search path.
Perhaps you should add the directory containing `libssh.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libssh' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lssh
---------------------------- [ANTICONF] --------------------------------
Configuration failed because libssh was not found. Try installing:
 * deb: libssh-dev (Debian, Ubuntu, etc)
 * rpm: libssh-devel (Fedora, EPEL)
 * brew: libssh (OSX)
If libssh is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libssh.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ------------------------------
<stdin>:1:10: fatal error: libssh/libssh.h: 没有那个文件或目录
compilation terminated.
-------------------------------------------------------------------------
ERROR: configuration failed for package ‘ssh’
* removing ‘/usr/lib/R/library/ssh’
* installing *source* package ‘DatabaseConnector’ ...
** 成功将‘DatabaseConnector’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** R
** 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
* DONE (DatabaseConnector)
* installing *source* package ‘aws.s3’ ...
** 成功将‘aws.s3’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aws.s3)
* installing *source* package ‘DBItest’ ...
** 成功将‘DBItest’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** R
** 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
* DONE (DBItest)
* installing *source* package ‘RSQLite’ ...
** 成功将‘RSQLite’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c DbColumn.cpp -o DbColumn.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c DbColumnDataSource.cpp -o DbColumnDataSource.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c DbColumnStorage.cpp -o DbColumnStorage.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c DbConnection.cpp -o DbConnection.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c DbDataFrame.cpp -o DbDataFrame.o
In file included from DbDataFrame.cpp:7:
vendor/boost/bind.hpp:41:1: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
 )
 ^
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c DbResult.cpp -o DbResult.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SqliteColumnDataSource.cpp -o SqliteColumnDataSource.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SqliteColumnDataSourceFactory.cpp -o SqliteColumnDataSourceFactory.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SqliteDataFrame.cpp -o SqliteDataFrame.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SqliteResult.cpp -o SqliteResult.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c SqliteResultImpl.cpp -o SqliteResultImpl.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c affinity.c -o affinity.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c connection.cpp -o connection.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ext-csv.c -o ext-csv.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ext-math.c -o ext-math.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ext-regexp.c -o ext-regexp.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ext-series.c -o ext-series.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c extensions.cpp -o extensions.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c import-file.c -o import-file.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c result.cpp -o result.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c rsqlite.cpp -o rsqlite.o
gcc -I"/usr/share/R/include" -DNDEBUG -I. -Ivendor -Ivendor/extensions -Ivendor/sqlite3 -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DSQLITE_USE_URI=1 -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/usr/lib/R/library/plogr/include' -I'/usr/lib/R/library/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c vendor/sqlite3/sqlite3.c -o vendor/sqlite3/sqlite3.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o RSQLite.so DbColumn.o DbColumnDataSource.o DbColumnDataSourceFactory.o DbColumnStorage.o DbConnection.o DbDataFrame.o DbResult.o RcppExports.o SqliteColumnDataSource.o SqliteColumnDataSourceFactory.o SqliteDataFrame.o SqliteResult.o SqliteResultImpl.o affinity.o connection.o ext-csv.o ext-math.o ext-regexp.o ext-series.o extensions.o import-file.o result.o rsqlite.o vendor/sqlite3/sqlite3.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/library/RSQLite/libs
** R
** 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
* DONE (RSQLite)
* installing *source* package ‘Andromeda’ ...
** 成功将‘Andromeda’程序包解包并MD5和检查
staged installation is only possible with locking
** using non-staged installation
** R
** 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
* DONE (Andromeda)

下载的程序包在
        ‘/tmp/Rtmp1Mod4N/downloaded_packages’里
更新'.Library'里的HTML程序包列表
Making 'packages.html' ... 做完了。
Warning message:
In install.packages(c("DatabaseConnector"), repos = "https://cran.rstudio.com",  :
  安装程序包‘ssh’时退出狀態的值不是0

Relevant topic with regards sparklyr, high volume dataset handling, quantitative analysis, high frequency trading, database :

englianhu commented 2 years ago 
sudo apt install libssh-dev -y
sudo su - -c "R -e \"install.packages(c('DatabaseConnector'), repos = 'https://cran.rstudio.com', lib = '/usr/lib/R/library', dependencies = TRUE, INSTALL_opts = '--no-lock')\""