Hi all
i have several problem in package download
The R version I used is R version 3.4.4 under Ubuntu 14.04.5 LTS
For somereason l can't not chang the system without premission from sudo
I can download most package like vegan, parallel, foreach, Kendall, MASS, dplyr …….
but some special package i cannot install
There are three types of problems i meet
First was package ‘xxxxx’ is not available (for R version 3.4.4)
For example
> install.packages("rlang")
Installing package into ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning message:
package ‘rlang’ is not available (for R version 3.4.4)
The second is package ‘xxx’ had non-zero exit status
For example
> install.packages("rEDM")
Installing package into ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rEDM_1.14.0.tar.gz'
Content type 'application/x-gzip' length 2035950 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘rEDM’ ...
** package ‘rEDM’ successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I ./cppEDM/src/ -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c CCM.cpp -o CCM.o
In file included from /home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread.h:12:0,
from RcppEDMCommon.h:12,
from CCM.cpp:2:
/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread/Thread.hpp: In lambda function:
/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread/Thread.hpp:43:19: error: parameter packs not expanded with ‘...’:
f(args...);
^
/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread/Thread.hpp:43:19: note: ‘args’
/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread/Thread.hpp:43:23: error: expansion pattern ‘args’ contains no argument packs
f(args...);
^
In file included from /home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread/ThreadPool.hpp:12:0,
from /home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread.h:13,
from RcppEDMCommon.h:12,
from CCM.cpp:2:
/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread/quickpool.hpp: In function ‘void* quickpool::mem::aligned::alloc(size_t, size_t)’:
/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/RcppThread/include/RcppThread/quickpool.hpp:131:11: error: ‘align’ is not a member of ‘std’
(void)std::align(alignment, size, p_algn, space);
^
make: *** [CCM.o] Error 1
ERROR: compilation failed for package ‘rEDM’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/rEDM’
The downloaded source packages are in
‘/tmp/RtmpJqytzh/downloaded_packages’
Warning message:
In install.packages("rEDM") :
installation of package ‘rEDM’ had non-zero exit status
The third was complex and i cannot name it
> install.packages("devtools")
Installing package into ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning: dependencies ‘rlang’, ‘httr’ are not available
also installing the dependencies ‘credentials’, ‘httr2’, ‘httpuv’, ‘systemfonts’, ‘textshaping’, ‘curl’, ‘gert’, ‘gh’, ‘shiny’, ‘ragg’, ‘rmarkdown’, ‘xml2’, ‘stringr’, ‘usethis’, ‘miniUI’, ‘pkgdown’, ‘profvis’, ‘rcmdcheck’, ‘roxygen2’, ‘rversions’, ‘urlchecker’
trying URL 'https://cloud.r-project.org/src/contrib/credentials_1.3.2.tar.gz'
Content type 'application/x-gzip' length 230070 bytes (224 KB)
==================================================
downloaded 224 KB
trying URL 'https://cloud.r-project.org/src/contrib/httr2_0.2.2.tar.gz'
Content type 'application/x-gzip' length 121360 bytes (118 KB)
==================================================
downloaded 118 KB
trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.9.tar.gz'
Content type 'application/x-gzip' length 1875081 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/systemfonts_1.0.4.tar.gz'
Content type 'application/x-gzip' length 81757 bytes (79 KB)
==================================================
downloaded 79 KB
trying URL 'https://cloud.r-project.org/src/contrib/textshaping_0.3.6.tar.gz'
Content type 'application/x-gzip' length 35722 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'https://cloud.r-project.org/src/contrib/curl_5.0.0.tar.gz'
Content type 'application/x-gzip' length 682047 bytes (666 KB)
==================================================
downloaded 666 KB
trying URL 'https://cloud.r-project.org/src/contrib/gert_1.9.2.tar.gz'
Content type 'application/x-gzip' length 121088 bytes (118 KB)
==================================================
downloaded 118 KB
trying URL 'https://cloud.r-project.org/src/contrib/gh_1.4.0.tar.gz'
Content type 'application/x-gzip' length 41214 bytes (40 KB)
==================================================
downloaded 40 KB
trying URL 'https://cloud.r-project.org/src/contrib/shiny_1.7.4.tar.gz'
Content type 'application/x-gzip' length 2476288 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
trying URL 'https://cloud.r-project.org/src/contrib/ragg_1.2.5.tar.gz'
Content type 'application/x-gzip' length 427859 bytes (417 KB)
==================================================
downloaded 417 KB
trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.21.tar.gz'
Content type 'application/x-gzip' length 2121971 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.3.tar.gz'
Content type 'application/x-gzip' length 283965 bytes (277 KB)
==================================================
downloaded 277 KB
trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.5.0.tar.gz'
Content type 'application/x-gzip' length 175699 bytes (171 KB)
==================================================
downloaded 171 KB
trying URL 'https://cloud.r-project.org/src/contrib/usethis_2.1.6.tar.gz'
Content type 'application/x-gzip' length 342349 bytes (334 KB)
==================================================
downloaded 334 KB
trying URL 'https://cloud.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz'
Content type 'application/x-gzip' length 97958 bytes (95 KB)
==================================================
downloaded 95 KB
trying URL 'https://cloud.r-project.org/src/contrib/pkgdown_2.0.7.tar.gz'
Content type 'application/x-gzip' length 871465 bytes (851 KB)
==================================================
downloaded 851 KB
trying URL 'https://cloud.r-project.org/src/contrib/profvis_0.3.7.tar.gz'
Content type 'application/x-gzip' length 142546 bytes (139 KB)
==================================================
downloaded 139 KB
trying URL 'https://cloud.r-project.org/src/contrib/rcmdcheck_1.4.0.tar.gz'
Content type 'application/x-gzip' length 73522 bytes (71 KB)
==================================================
downloaded 71 KB
trying URL 'https://cloud.r-project.org/src/contrib/roxygen2_7.2.3.tar.gz'
Content type 'application/x-gzip' length 279442 bytes (272 KB)
==================================================
downloaded 272 KB
trying URL 'https://cloud.r-project.org/src/contrib/rversions_2.1.2.tar.gz'
Content type 'application/x-gzip' length 42135 bytes (41 KB)
==================================================
downloaded 41 KB
trying URL 'https://cloud.r-project.org/src/contrib/urlchecker_1.0.1.tar.gz'
Content type 'application/x-gzip' length 13340 bytes (13 KB)
==================================================
downloaded 13 KB
trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.4.5.tar.gz'
Content type 'application/x-gzip' length 374718 bytes (365 KB)
==================================================
downloaded 365 KB
* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports-legacy.cpp -o RcppExports-legacy.o
g++ -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -I"/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c callback.cpp -o callback.o
In file included from callback.cpp:1:0:
callback.h:21:3: error: ‘function’ in namespace ‘std’ does not name a type
std::function<void (void)> fun;
^
callback.h:24:36: error: expected ‘)’ before ‘<’ token
StdFunctionCallback(std::function<void (void)> fun)
^
callback.h: In member function ‘virtual void StdFunctionCallback::operator()()’:
callback.h:29:9: error: ‘fun’ was not declared in this scope
fun();
^
callback.h: At global scope:
callback.h:34:24: error: variable or field ‘invoke_later’ declared void
void invoke_later(std::function<void(void)> f, double secs = 0);
^
callback.h:34:19: error: ‘function’ is not a member of ‘std’
void invoke_later(std::function<void(void)> f, double secs = 0);
^
callback.h:34:33: error: expected primary-expression before ‘void’
void invoke_later(std::function<void(void)> f, double secs = 0);
^
callback.h:34:48: error: expected primary-expression before ‘double’
void invoke_later(std::function<void(void)> f, double secs = 0);
^
callback.cpp:12:24: error: variable or field ‘invoke_later’ declared void
void invoke_later(std::function<void(void)> f, double secs) {
^
callback.cpp:12:19: error: ‘function’ is not a member of ‘std’
void invoke_later(std::function<void(void)> f, double secs) {
^
callback.cpp:12:33: error: expected primary-expression before ‘void’
void invoke_later(std::function<void(void)> f, double secs) {
^
callback.cpp:12:48: error: expected primary-expression before ‘double’
void invoke_later(std::function<void(void)> f, double secs) {
^
make: *** [callback.o] Error 1
ERROR: compilation failed for package ‘httpuv’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/httpuv’
* installing *source* package ‘systemfonts’ ...
** package ‘systemfonts’ successfully unpacked and MD5 sums checked
Package fontconfig was not found in the pkg-config search path.
Perhaps you should add the directory containing `fontconfig.pc'
to the PKG_CONFIG_PATH environment variable
No package 'fontconfig' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lfontconfig -lfreetype
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the fontconfig freetype2 library. Try installing:
* deb: libfontconfig1-dev (Debian, Ubuntu, etc)
* rpm: fontconfig-devel (Fedora, EPEL)
* csw: fontconfig_dev (Solaris)
* brew: freetype (OSX)
If fontconfig freetype2 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.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>:1:35: fatal error: fontconfig/fontconfig.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘systemfonts’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/systemfonts’
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
--------------------------- [ANTICONF] --------------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.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>:1:23: fatal error: curl/curl.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/curl’
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
* deb: libxml2-dev (Debian, Ubuntu, etc)
* rpm: libxml2-devel (Fedora, CentOS, RHEL)
* csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.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: configuration failed for package ‘xml2’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/xml2’
ERROR: dependency ‘rlang’ is not available for package ‘stringr’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/stringr’
ERROR: dependency ‘curl’ is not available for package ‘credentials’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/credentials’
ERROR: dependencies ‘curl’, ‘rlang’ are not available for package ‘httr2’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/httr2’
ERROR: dependency ‘systemfonts’ is not available for package ‘textshaping’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/textshaping’
ERROR: dependencies ‘httpuv’, ‘rlang’ are not available for package ‘shiny’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/shiny’
ERROR: dependency ‘stringr’ is not available for package ‘rmarkdown’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/rmarkdown’
ERROR: dependency ‘stringr’ is not available for package ‘profvis’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/profvis’
ERROR: dependency ‘curl’ is not available for package ‘rcmdcheck’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/rcmdcheck’
ERROR: dependencies ‘rlang’, ‘stringr’, ‘xml2’ are not available for package ‘roxygen2’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/roxygen2’
ERROR: dependencies ‘curl’, ‘xml2’ are not available for package ‘rversions’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/rversions’
ERROR: dependencies ‘curl’, ‘xml2’ are not available for package ‘urlchecker’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/urlchecker’
ERROR: dependency ‘credentials’ is not available for package ‘gert’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/gert’
ERROR: dependencies ‘httr2’, ‘rlang’ are not available for package ‘gh’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/gh’
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/ragg’
ERROR: dependency ‘shiny’ is not available for package ‘miniUI’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/miniUI’
ERROR: dependencies ‘curl’, ‘gert’, ‘gh’, ‘rlang’ are not available for package ‘usethis’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/usethis’
ERROR: dependencies ‘httr’, ‘ragg’, ‘rlang’, ‘rmarkdown’, ‘xml2’ are not available for package ‘pkgdown’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/pkgdown’
ERROR: dependencies ‘usethis’, ‘miniUI’, ‘pkgdown’, ‘profvis’, ‘rcmdcheck’, ‘rlang’, ‘roxygen2’, ‘rversions’, ‘urlchecker’ are not available for package ‘devtools’
* removing ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4/devtools’
The downloaded source packages are in
‘/tmp/RtmpDyCkjX/downloaded_packages’
There were 22 warnings (use warnings() to see them)
and i try to fix it by the following instruction
Configuration failed to find the fontconfig freetype2 library. Try installing:
- deb: libfontconfig1-dev (Debian, Ubuntu, etc)
it still now work
> install.packages("deb")
Installing package into ‘/home/chaojuichang/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning message:
package ‘deb’ is not available (for R version 3.4.4)
i know it is hard to do a lot of things in the older version of R
but is it possible to slove the problem i meet ?
Any comments and suggestions will be appreciated
Sincerely