To install the packages from source, you need to install make, gcc, and g++: sudo apt install make sudo apt install gcc sudo apt install g++
then try installing them again On Thu, Oct 6, 2022 at 2:54 AM Rhon Calderon, Eric <[email protected]> wrote: > > 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 > > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
