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Rhon Calderon, Eric

2022-Oct-05 20:02 UTC

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

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 (G?ttingen) [https]
40: Germany (M?nster) [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 Coru?a) [https]
63: Spain (Madrid) [https]
64: Sweden (Bor?s) [https]
65: Sweden (Ume?) [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]]

Andrew Simmons

2022-Oct-06 06:57 UTC

head link

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

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 at 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 (G?ttingen) [https]
> 40: Germany (M?nster) [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 Coru?a) [https]
> 63: Spain (Madrid) [https]
> 64: Sweden (Bor?s) [https]
> 65: Sweden (Ume?) [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]]
>
> ______________________________________________
> R-help at r-project.org 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.

Ivan Krylov

2022-Oct-06 07:26 UTC

head link

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

On Wed, 5 Oct 2022 20:02:02 +0000
"Rhon Calderon, Eric" <Eric.RhonCalderon at
pennmedicine.upenn.edu> wrote:
> automake found. Running autoupdate and autogen.sh.
<...>> + libtoolize --copy
> autogen.sh: line 43: libtoolize: command not found
Since you have automake installed, you also need libtool
<https://www.gnu.org/software/libtool/> installed in order to compile
this particular package from source. Depending on the HPC, there may be
a particular command to "activate" the installation already made by
the
HPC administrator.

I guess you could also report this as a bug in devtools: they check for
automake but not libtool. If you can temporarily chmod -x automake, the
installation should succeed too, because then the package will not try
to regenerate its build system. I don't see why they even try to do
that, but maybe that's a workaround for some kind of compatibility
problem.
> 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
Make sure your automake installation is working. I think the error is
caused by the previous error and may go away once you install libtool,
but I may be mistaken regarding that.

Do Bioconductor packages really depend on devtools? What do their
errors look like?

-- 
Best regards,
Ivan

R help - Oct 2022 - Help installing devtools plus other packages in R terminal

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

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

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