Build problems on CRAN Fedora machines

[wch]

https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/httpuv-00install.html

The problem seems to be that it's trying to re-run automake.

* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/httpuv/src'
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c RcppExports-legacy.cpp -o RcppExports-legacy.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c callback.cpp -o callback.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c callbackqueue.cpp -o callbackqueue.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c filedatasource-unix.cpp -o filedatasource-unix.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c filedatasource-win.cpp -o filedatasource-win.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c http.cpp -o http.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c httprequest.cpp -o httprequest.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c httpresponse.cpp -o httpresponse.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c httpuv.cpp -o httpuv.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c md5.c -o md5.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c set_invalid_parameter.c -o set_invalid_parameter.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c socket.cpp -o socket.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c thread.cpp -o thread.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c utils.cpp -o utils.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c uvutil.cpp -o uvutil.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c webapplication.cpp -o webapplication.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c websockets-base.cpp -o websockets-base.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c websockets-hixie76.cpp -o websockets-hixie76.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c websockets-hybi03.cpp -o websockets-hybi03.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c websockets-ietf.cpp -o websockets-ietf.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c websockets.cpp -o websockets.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c http-parser/http_parser.c -o http-parser/http_parser.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c sha1/sha1.c -o sha1/sha1.o
clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -fvisibility=hidden -I"/data/gannet/ripley/R/test-clang/Rcpp/include" -I"/data/gannet/ripley/R/test-clang/BH/include" -I"/data/gannet/ripley/R/test-clang/later/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c base64/base64.cpp -o base64/base64.o
(cd libuv \
	&& touch Makefile.in aclocal.m4 configure m4/lt~obsolete.m4 \
	&& CC="clang" CFLAGS="-g -O3 -Wall -pedantic  -fpic -fvisibility=hidden" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/clang/lib64 -L/usr/local/lib64" ./configure "--quiet")
make --directory=libuv \
	HAVE_DTRACE=0
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/httpuv/src/libuv'
 cd . && /bin/sh /data/gannet/ripley/R/packages/tests-clang/httpuv/src/libuv/missing automake-1.15 --foreign
configure.ac:21: error: version mismatch.  This is Automake 1.15,
configure.ac:21: but the definition used by this AM_INIT_AUTOMAKE
configure.ac:21: comes from Automake 1.15.1.  You should recreate
configure.ac:21: aclocal.m4 with aclocal and run automake again.
WARNING: 'automake-1.15' is probably too old.
         You should only need it if you modified 'Makefile.am' or
         'configure.ac' or m4 files included by 'configure.ac'.
         The 'automake' program is part of the GNU Automake package:
         <http://www.gnu.org/software/automake>
         It also requires GNU Autoconf, GNU m4 and Perl in order to run:
         <http://www.gnu.org/software/autoconf>
         <http://www.gnu.org/software/m4/>
         <http://www.perl.org/>
make[2]: *** [Makefile:1093: Makefile.in] Error 1
make[2]: Failed to remake makefile 'Makefile'.
  CC       src/libuv_la-fs-poll.lo
  CC       src/libuv_la-inet.lo
  CC       src/libuv_la-threadpool.lo
  CC       src/libuv_la-uv-common.lo
  CC       src/libuv_la-version.lo
  CC       src/unix/libuv_la-async.lo
  CC       src/unix/libuv_la-core.lo
  CC       src/unix/libuv_la-dl.lo
  CC       src/unix/libuv_la-fs.lo
  CC       src/unix/libuv_la-getaddrinfo.lo
  CC       src/unix/libuv_la-getnameinfo.lo
  CC       src/unix/libuv_la-loop-watcher.lo
  CC       src/unix/libuv_la-loop.lo
  CC       src/unix/libuv_la-pipe.lo
  CC       src/unix/libuv_la-poll.lo
  CC       src/unix/libuv_la-process.lo
  CC       src/unix/libuv_la-signal.lo
  CC       src/unix/libuv_la-stream.lo
  CC       src/unix/libuv_la-tcp.lo
  CC       src/unix/libuv_la-thread.lo
  CC       src/unix/libuv_la-timer.lo
  CC       src/unix/libuv_la-tty.lo
  CC       src/unix/libuv_la-udp.lo
  CC       src/unix/libuv_la-linux-core.lo
  CC       src/unix/libuv_la-linux-inotify.lo
  CC       src/unix/libuv_la-linux-syscalls.lo
  CC       src/unix/libuv_la-procfs-exepath.lo
  CC       src/unix/libuv_la-proctitle.lo
  CC       src/unix/libuv_la-sysinfo-loadavg.lo
  CC       src/unix/libuv_la-sysinfo-memory.lo
  CCLD     libuv.la
make[2]: Target 'all' not remade because of errors.
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/httpuv/src/libuv'
make[1]: *** [Makevars:53: libuv/.libs/libuv.a] Error 2
make[1]: Target 'httpuv.so' not remade because of errors.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/httpuv/src'
ERROR: compilation failed for package ‘httpuv’
* removing ‘/data/gannet/ripley/R/packages/tests-clang/httpuv.Rcheck/httpuv’

---

I haven't been able to reproduce the problem yet. Here's a Dockerfile with Centos 6.7, and build commands (the build succeeds).

Dockerfile:

FROM centos:centos6.7

RUN yum -y install epel-release
RUN yum update -y && yum clean all
RUN yum install -y locales tar


RUN yum groupinstall -y "Development Tools"

RUN yum install -y wget git xml2 libxml2-devel curl curl-devel openssl-devel

WORKDIR /home/root
RUN yum install -y R

ENV LANG en_US.UTF-8

RUN yum install -y openssl098e passwd pandoc

RUN echo "MAKEFLAGS=-j4" > ~/.Renviron

RUN R --quiet -e "install.packages('devtools', repos='https://cloud.r-project.org')"

Build commands:

docker build -t r-centos6 .
docker run --rm -ti r-centos6 /bin/bash
R --quiet
install.packages('httpuv', repos='https://cloud.r-project.org')