[R] Help installing devtools plus other packages in R terminal

Thu Oct 6 08:57:41 CEST 2022

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
<Eric.RhonCalderon using pennmedicine.upenn.edu> 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]]
>
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