[R] Help installing devtools plus other packages in R terminal
Rhon Calderon, Eric
Er|c@RhonC@|deron @end|ng |rom pennmed|c|ne@upenn@edu
Wed Oct 5 22:02:02 CEST 2022
Hi,
I am using R in my HPC terminal. After many tries, I was able to install and exec successfully R on my HPC but now I cannot install devtools and other dependencies. I need some of theses packages to install some others from bioconductor. I was wondering if anybody has a solution.
The script I got from my R session is (the highlighted part is the errors I keep getting):
> install.packages('devtools')
Installing package into ‘/home/ericrhon/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
3: Australia (Melbourne 1) [https]
4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https]
6: Austria [https]
7: Belgium (Brussels) [https]
8: Brazil (PR) [https]
9: Brazil (RJ) [https]
10: Brazil (SP 1) [https]
11: Brazil (SP 2) [https]
12: Bulgaria [https]
13: Canada (MB) [https]
14: Canada (ON 3) [https]
15: Chile (Santiago) [https]
16: China (Beijing 2) [https]
17: China (Beijing 3) [https]
18: China (Hefei) [https]
19: China (Hong Kong) [https]
20: China (Guangzhou) [https]
21: China (Lanzhou) [https]
22: China (Nanjing) [https]
23: China (Shanghai 2) [https]
24: China (Shenzhen) [https]
25: Colombia (Cali) [https]
26: Costa Rica [https]
27: Cyprus [https]
28: Czech Republic [https]
29: Denmark [https]
30: East Asia [https]
31: Ecuador (Cuenca) [https]
32: Ecuador (Quito) [https]
33: France (Lyon 1) [https]
34: France (Lyon 2) [https]
35: France (Marseille) [https]
36: France (Paris 1) [https]
37: Germany (Erlangen) [https]
38: Germany (Leipzig) [https]
39: Germany (Göttingen) [https]
40: Germany (Münster) [https]
41: Germany (Regensburg) [https]
42: Greece [https]
43: Hungary [https]
44: Iceland [https]
45: India [https]
46: Indonesia (Banda Aceh) [https]
47: Iran (Mashhad) [https]
48: Italy (Milano) [https]
49: Italy (Padua) [https]
50: Japan (Tokyo) [https]
51: Japan (Yonezawa) [https]
52: Korea (Gyeongsan-si) [https]
53: Korea (Ulsan) [https]
54: Malaysia [https]
55: Mexico (Mexico City) [https]
56: Mexico (Texcoco) [https]
57: Morocco [https]
58: Netherlands (Dronten) [https]
59: New Zealand [https]
60: Norway [https]
61: South Africa (Johannesburg) [https]
62: Spain (A Coruña) [https]
63: Spain (Madrid) [https]
64: Sweden (Borås) [https]
65: Sweden (Umeå) [https]
66: Switzerland [https]
67: Taiwan (Taipei) [https]
68: Turkey (Denizli) [https]
69: Turkey (Istanbul) [https]
70: Turkey (Mersin) [https]
71: UK (Bristol) [https]
72: UK (London 1) [https]
73: USA (IA) [https]
74: USA (MI) [https]
75: USA (MO) [https]
76: USA (OH) [https]
77: USA (OR) [https]
78: USA (TN) [https]
79: USA (TX 1) [https]
80: Uruguay [https]
81: (other mirrors)
Selection: 1
also installing the dependencies ‘httpuv’, ‘shiny’, ‘miniUI’
trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.6.tar.gz'
Content type 'application/x-gzip' length 1875264 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/shiny_1.7.2.tar.gz'
Content type 'application/x-gzip' length 2982507 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
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/devtools_2.4.4.tar.gz'
Content type 'application/x-gzip' length 374492 bytes (365 KB)
==================================================
downloaded 365 KB
* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c RcppExports-legacy.cpp -o RcppExports-legacy.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c callback.cpp -o callback.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c callbackqueue.cpp -o callbackqueue.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c filedatasource-unix.cpp -o filedatasource-unix.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c filedatasource-win.cpp -o filedatasource-win.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c fs.cpp -o fs.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c gzipdatasource.cpp -o gzipdatasource.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c http.cpp -o http.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c httprequest.cpp -o httprequest.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c httpresponse.cpp -o httpresponse.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c httpuv.cpp -o httpuv.o
gcc -std=gnu11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c md5.c -o md5.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c mime.cpp -o mime.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c socket.cpp -o socket.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c staticpath.cpp -o staticpath.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c thread.cpp -o thread.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c timegm.cpp -o timegm.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c utils.cpp -o utils.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c uvutil.cpp -o uvutil.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c webapplication.cpp -o webapplication.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-base.cpp -o websockets-base.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-hixie76.cpp -o websockets-hixie76.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-hybi03.cpp -o websockets-hybi03.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets-ietf.cpp -o websockets-ietf.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c websockets.cpp -o websockets.o
g++ -std=gnu++11 -I"/home/ericrhon/R/4.2/R-4.2.1/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/ericrhon/R/4.2/R-4.2.1/library/Rcpp/include' -I'/home/ericrhon/R/4.2/R-4.2.1/library/later/include' -I/usr/local/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -c winutils.cpp -o winutils.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
cd libuv; \
if ! command -v automake >/dev/null 2>&1 ; then \
echo "automake not found. Touching files so configure will not try to run automake."; \
touch aclocal.m4; \
touch -r aclocal.m4 configure Makefile.in; \
else \
echo "automake found. Running autoupdate and autogen.sh."; \
autoupdate; \
sh autogen.sh; \
fi; \
chmod +x configure; \
CC="gcc -std=gnu11" CFLAGS="-g -O2 -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib64" ./configure "--quiet"
automake found. Running autoupdate and autogen.sh.
aclocal.m4:17: warning: this file was generated for autoconf 2.71.
You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.
+ libtoolize --copy
autogen.sh: line 43: libtoolize: command not found
make --directory=libuv \
HAVE_DTRACE=0
make[1]: Entering directory `/tmp/RtmpMjF6Ns/R.INSTALL4a3cb2204b0da/httpuv/src/libuv'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh '/tmp/RtmpMjF6Ns/R.INSTALL4a3cb2204b0da/httpuv/src/libuv/missing' aclocal-1.16 -I m4
/tmp/RtmpMjF6Ns/R.INSTALL4a3cb2204b0da/httpuv/src/libuv/missing: line 81: aclocal-1.16: command not found
WARNING: 'aclocal-1.16' is missing on your system.
You should only need it if you modified 'acinclude.m4' or
'configure.ac' or m4 files included by 'configure.ac'.
The 'aclocal' program is part of the GNU Automake package:
<https://www.gnu.org/software/automake>
It also requires GNU Autoconf, GNU m4 and Perl in order to run:
<https://www.gnu.org/software/autoconf>
<https://www.gnu.org/software/m4/>
<https://www.perl.org/>
make[1]: *** [aclocal.m4] Error 127
make[1]: Leaving directory `/tmp/RtmpMjF6Ns/R.INSTALL4a3cb2204b0da/httpuv/src/libuv'
make: *** [libuv/.libs/libuv.a] Error 2
ERROR: compilation failed for package ‘httpuv’
* removing ‘/home/ericrhon/R/x86_64-pc-linux-gnu-library/4.2/httpuv’
ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
* removing ‘/home/ericrhon/R/x86_64-pc-linux-gnu-library/4.2/shiny’
ERROR: dependency ‘shiny’ is not available for package ‘miniUI’
* removing ‘/home/ericrhon/R/x86_64-pc-linux-gnu-library/4.2/miniUI’
ERROR: dependency ‘miniUI’ is not available for package ‘devtools’
* removing ‘/home/ericrhon/R/x86_64-pc-linux-gnu-library/4.2/devtools’
The downloaded source packages are in
‘/tmp/RtmpZELkpr/downloaded_packages’
Warning messages:
1: In install.packages("devtools") :
installation of package ‘httpuv’ had non-zero exit status
2: In install.packages("devtools") :
installation of package ‘shiny’ had non-zero exit status
3: In install.packages("devtools") :
installation of package ‘miniUI’ had non-zero exit status
4: In install.packages("devtools") :
installation of package ‘devtools’ had non-zero exit status
Thanks.
Eric
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