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Compiling of readr 1.2.1 fails on (Ubuntu) linux multiple architecture R installation #922

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BerwinTurlach opened this issue Nov 23, 2018 · 18 comments

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@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 23, 2018

Hello all,

Today, update.packages() wanted to update readr on my machine from version 1.1.1 to 1.2.1. However the installation was not successful. I have an R installation with two architectures (32 bit and 64bit) and, apparently, for some reason a 64 bit dynamic object ended up in the 32 bit architecture so that at the end of the installation process the testing if installed package can be loaded failed. Complete output of the installation process is attached below.

Cheers,
Berwin

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu/64 (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=C              
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sos_2.0-0  brew_1.0-6

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       digest_0.6.18    rprojroot_1.3-2  jsonlite_1.5     backports_1.1.2  magrittr_1.5     evaluate_0.12   
 [8] stringi_1.2.4    rmarkdown_1.10   tools_3.5.1      stringr_1.3.1    yaml_2.2.0       rsconnect_0.8.11 compiler_3.5.1  
[15] base64enc_0.1-3  htmltools_0.3.6  knitr_1.20      
* installing *source* package ‘readr’ ...
** package ‘readr’ successfully unpacked and MD5 sums checked
** libs
*** arch - 32
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Collector.cpp -o Collector.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c CollectorGuess.cpp -o CollectorGuess.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Iconv.cpp -o Iconv.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c LocaleInfo.cpp -o LocaleInfo.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c RcppExports.cpp -o RcppExports.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Reader.cpp -o Reader.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Source.cpp -o Source.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Tokenizer.cpp -o Tokenizer.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c TokenizerDelim.cpp -o TokenizerDelim.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c TokenizerFwf.cpp -o TokenizerFwf.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c TokenizerWs.cpp -o TokenizerWs.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c connection.cpp -o connection.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c datetime.cpp -o datetime.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu   -fpic  -g -O2  -c grisu3.c -o grisu3.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu   -fpic  -g -O2  -c init.c -o init.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu   -fpic  -g -O2  -c localtime.c -o localtime.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c parse.cpp -o parse.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c read.cpp -o read.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c type_convert.cpp -o type_convert.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c write.cpp -o write.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c write_connection.cpp -o write_connection.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c write_delim.cpp -o write_delim.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/opt/src/CURL32/usr/include/i386-linux-gnu   -fpic  -g -O2  -c rcon/connection.c -o rcon/connection.o
g++ -m32  -shared -L"/opt/R/R-3.5.1/lib/R/lib/32" -L/usr/local/lib -o ../inst/rcon/librcon.so rcon/connection.o
g++ -m32 -shared -L/opt/R/R-3.5.1/lib/R/lib/32 -L/usr/local/lib -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o RcppExports.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o datetime.o grisu3.o init.o localtime.o parse.o read.o type_convert.o write.o write_connection.o write_delim.o -L. -lrcon -L../inst/rcon -Wl,-rpath,/opt/R/R-3.5.1/lib/R/library/readr/rcon -L/opt/R/R-3.5.1/lib/R/lib/32 -lR
installing via 'install.libs.R' to /opt/R/R-3.5.1/lib/R/library/readr
*** arch - 64
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Collector.cpp -o Collector.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c CollectorGuess.cpp -o CollectorGuess.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Iconv.cpp -o Iconv.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c LocaleInfo.cpp -o LocaleInfo.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c RcppExports.cpp -o RcppExports.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Reader.cpp -o Reader.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Source.cpp -o Source.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c Tokenizer.cpp -o Tokenizer.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c TokenizerDelim.cpp -o TokenizerDelim.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c TokenizerFwf.cpp -o TokenizerFwf.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c TokenizerWs.cpp -o TokenizerWs.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c connection.cpp -o connection.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c datetime.cpp -o datetime.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c grisu3.c -o grisu3.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c localtime.c -o localtime.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c parse.cpp -o parse.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c read.cpp -o read.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c type_convert.cpp -o type_convert.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c write.cpp -o write.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c write_connection.cpp -o write_connection.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c write_delim.cpp -o write_delim.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c rcon/connection.c -o rcon/connection.o
g++  -shared -L"/opt/R/R-3.5.1/lib/R/lib/64" -L/usr/local/lib -o ../inst/rcon/librcon.so rcon/connection.o
g++ -shared -L/opt/R/R-3.5.1/lib/R/lib/64 -L/usr/local/lib -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o RcppExports.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o datetime.o grisu3.o init.o localtime.o parse.o read.o type_convert.o write.o write_connection.o write_delim.o -L. -lrcon -L../inst/rcon -Wl,-rpath,/opt/R/R-3.5.1/lib/R/library/readr/rcon -L/opt/R/R-3.5.1/lib/R/lib/64 -lR
installing via 'install.libs.R' to /opt/R/R-3.5.1/lib/R/library/readr
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - 32
Error: package or namespace load failed for ‘readr’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/R/R-3.5.1/lib/R/library/readr/libs/32/readr.so':
  librcon.so: wrong ELF class: ELFCLASS64
Error: loading failed
Execution halted
*** arch - 64
ERROR: loading failed for ‘32’
* removing ‘/opt/R/R-3.5.1/lib/R/library/readr’
* restoring previous ‘/opt/R/R-3.5.1/lib/R/library/readr’
Warning in install.packages :
  installation of package ‘readr’ had non-zero exit status
@tarmenic
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@tarmenic tarmenic commented Nov 23, 2018

That is pretty much what is currently being discussed in Issue #919, I believe.

@jimhester
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@jimhester jimhester commented Nov 23, 2018

I have never heard of anyone outside of WIndows having two architectures, I can look into fixing this but it may take some time.

@eddelbuettel
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@eddelbuettel eddelbuettel commented Nov 27, 2018

@jimhester: See eg

It's a pretty old initiative but it never really took off. But i386 and x86_64 can coexists easily and some distros stress it more than others. On my Ubuntu system I see /usr/lib/x86_64-linux-gnu as well as /usr/lib32 even though I did not make a point about multiarch.

@eddelbuettel
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@eddelbuettel eddelbuettel commented Nov 27, 2018

@BerwinTurlach The current readr fails to build / install as a standard Debian package, even in single arch. That risked blocking all of tidyverse so I cooked up a simple workaround essentialy by doing away with the 2nd library.

@jimhester
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@jimhester jimhester commented Nov 28, 2018

@BerwinTurlach I think this would be fixed by the code in 922

Could you try installing it on your machine? I don't really have a easy way to test R installed with multiple architectures on linux

devtools::install_github("tidyverse/readr@922")

@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 28, 2018

@jimhester thank you for trying to fix this problem. The proposed changes do not seem to be sufficient, see attached output below.
Not sure whether it would be sufficient to change in the makefile the line

$(SHLIB): ../inst/rcon/librcon.so

to

$(SHLIB): ../inst/rcon$(R_ARCH)/librcon.so

My knowledge of writing makefiles is getting a bit rusty. :)

Output from attempting to install readr@922:

> devtools::install_github("tidyverse/readr@922")
Downloading GitHub repo tidyverse/readr@922
✔  checking for file ‘/tmp/RtmpPFqXpP/remotes22de44aa4d8d/tidyverse-readr-d4cb2a1/DESCRIPTION’ ...
─  preparing ‘readr’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘readr_1.2.1.9000.tar.gz’
   
* installing *source* package ‘readr’ ...
** libs
*** arch - 32
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Collector.cpp -o Collector.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c CollectorGuess.cpp -o CollectorGuess.o
[...]
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write_connection.cpp -o write_connection.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write_delim.cpp -o write_delim.o
make: *** No rule to make target '../inst/rcon/librcon.so', needed by 'readr.so'.  Stop.
ERROR: compilation failed for package ‘readr’
* removing ‘/home/opt/R/R-3.5.1/lib/R/library/readr’
* restoring previous ‘/home/opt/R/R-3.5.1/lib/R/library/readr’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/RtmpPFqXpP/file22de571186cf/readr_1.2.1.9000.tar.gz’ had non-zero exit status

@jimhester
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@jimhester jimhester commented Nov 28, 2018

Thanks, sorry about that @BerwinTurlach, I have made this change, please try installing again.

@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 28, 2018

Thanks @jimhester, but problems seem to persist. As far as I can understand the output, when trying to create the target readr.so, the linker fails to find the library librcon.

> devtools::install_github("tidyverse/readr@922")
Downloading GitHub repo tidyverse/readr@922
✔  checking for file ‘/tmp/RtmpqYA5fu/remotes463c778d724d/tidyverse-readr-4fc68a4/DESCRIPTION’ ...
─  preparing ‘readr’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘readr_1.2.1.9000.tar.gz’
   
* installing *source* package ‘readr’ ...
** libs
*** arch - 32
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Collector.cpp -o Collector.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c CollectorGuess.cpp -o CollectorGuess.o
[...]
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c rcon/connection.c -o rcon/connection.o
mkdir -p ../inst/rcon/32
g++ -m32  -shared -L"/opt/R/R-3.5.1/lib/R/lib/32" -L/usr/local/lib -o ../inst/rcon/32/librcon.so rcon/connection.o
g++ -m32 -shared -L/opt/R/R-3.5.1/lib/R/lib/32 -L/usr/local/lib -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o RcppExports.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o datetime.o grisu3.o init.o localtime.o parse.o read.o type_convert.o write.o write_connection.o write_delim.o -L. -lrcon -L../inst/rcon -Wl,-rpath,$ORIGIN/../rcon/32 -L/opt/R/R-3.5.1/lib/R/lib/32 -lR
/usr/bin/ld: cannot find -lrcon
collect2: error: ld returned 1 exit status
/opt/R/R-3.5.1/lib/R/share/make/shlib.mk:6: recipe for target 'readr.so' failed
make: *** [readr.so] Error 1
ERROR: compilation failed for package ‘readr’
* removing ‘/home/opt/R/R-3.5.1/lib/R/library/readr’
* restoring previous ‘/home/opt/R/R-3.5.1/lib/R/library/readr’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/RtmpqYA5fu/file463c2a5418b3/readr_1.2.1.9000.tar.gz’ had non-zero exit status

@jimhester
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@jimhester jimhester commented Nov 28, 2018

Sorry, I missed one more place to add R_ARCH, please try it again (hopefully this is the last time).

@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 28, 2018

@jimhester the compilation phase now works fine, but it still fails when R tests whether the package can be loaded. Perhaps the problem is now the one pointed out earlier, or it needs the fix suggested by @eddelbuettel.

Output from an attempt to install the suggested fix:

> devtools::install_github("tidyverse/readr@922")
Downloading GitHub repo tidyverse/readr@922
✔  checking for file ‘/tmp/RtmpqYA5fu/remotes463c5a6e3325/tidyverse-readr-eb52dda/DESCRIPTION’ ...
─  preparing ‘readr’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘readr_1.2.1.9000.tar.gz’
   
* installing *source* package ‘readr’ ...
** libs
*** arch - 32
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Collector.cpp -o Collector.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c CollectorGuess.cpp -o CollectorGuess.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Iconv.cpp -o Iconv.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c LocaleInfo.cpp -o LocaleInfo.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Reader.cpp -o Reader.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Source.cpp -o Source.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Tokenizer.cpp -o Tokenizer.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c TokenizerDelim.cpp -o TokenizerDelim.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c TokenizerFwf.cpp -o TokenizerFwf.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c TokenizerWs.cpp -o TokenizerWs.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c connection.cpp -o connection.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c datetime.cpp -o datetime.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c grisu3.c -o grisu3.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c localtime.c -o localtime.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c parse.cpp -o parse.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c read.cpp -o read.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c type_convert.cpp -o type_convert.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write.cpp -o write.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write_connection.cpp -o write_connection.o
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write_delim.cpp -o write_delim.o
gcc -m32 -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c rcon/connection.c -o rcon/connection.o
mkdir -p ../inst/rcon/32
g++ -m32  -shared -L"/opt/R/R-3.5.1/lib/R/lib/32" -L/usr/local/lib -o ../inst/rcon/32/librcon.so rcon/connection.o
g++ -m32 -shared -L/opt/R/R-3.5.1/lib/R/lib/32 -L/usr/local/lib -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o RcppExports.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o datetime.o grisu3.o init.o localtime.o parse.o read.o type_convert.o write.o write_connection.o write_delim.o -L. -lrcon -L../inst/rcon/32 -Wl,-rpath,$ORIGIN/../rcon/32 -L/opt/R/R-3.5.1/lib/R/lib/32 -lR
installing via 'install.libs.R' to /home/opt/R/R-3.5.1/lib/R/library/readr
*** arch - 64
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Collector.cpp -o Collector.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c CollectorGuess.cpp -o CollectorGuess.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Iconv.cpp -o Iconv.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c LocaleInfo.cpp -o LocaleInfo.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Reader.cpp -o Reader.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Source.cpp -o Source.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Tokenizer.cpp -o Tokenizer.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c TokenizerDelim.cpp -o TokenizerDelim.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c TokenizerFwf.cpp -o TokenizerFwf.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c TokenizerWs.cpp -o TokenizerWs.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c connection.cpp -o connection.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c datetime.cpp -o datetime.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c grisu3.c -o grisu3.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c localtime.c -o localtime.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c parse.cpp -o parse.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c read.cpp -o read.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c type_convert.cpp -o type_convert.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write.cpp -o write.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write_connection.cpp -o write_connection.o
g++  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c write_delim.cpp -o write_delim.o
gcc -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/64" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -c rcon/connection.c -o rcon/connection.o
mkdir -p ../inst/rcon/64
g++  -shared -L"/opt/R/R-3.5.1/lib/R/lib/64" -L/usr/local/lib -o ../inst/rcon/64/librcon.so rcon/connection.o
g++ -shared -L/opt/R/R-3.5.1/lib/R/lib/64 -L/usr/local/lib -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o RcppExports.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o datetime.o grisu3.o init.o localtime.o parse.o read.o type_convert.o write.o write_connection.o write_delim.o -L. -lrcon -L../inst/rcon/64 -Wl,-rpath,$ORIGIN/../rcon/64 -L/opt/R/R-3.5.1/lib/R/lib/64 -lR
installing via 'install.libs.R' to /home/opt/R/R-3.5.1/lib/R/library/readr
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - 32
Error: package or namespace load failed for ‘readr’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/opt/R/R-3.5.1/lib/R/library/readr/libs/32/readr.so':
  librcon.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
*** arch - 64
Error: package or namespace load failed for ‘readr’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/opt/R/R-3.5.1/lib/R/library/readr/libs/64/readr.so':
  librcon.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed for ‘32’, ‘64’
* removing ‘/home/opt/R/R-3.5.1/lib/R/library/readr’
* restoring previous ‘/home/opt/R/R-3.5.1/lib/R/library/readr’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/tmp/RtmpqYA5fu/file463c7957c9bf/readr_1.2.1.9000.tar.gz’ had non-zero exit status

@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 28, 2018

@jimhester
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@jimhester jimhester commented Nov 28, 2018

@BerwinTurlach if you could try installing from that branch one final time I believe this should now be fixed.

@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 29, 2018

@jimhester not sure what is happening now, but the result is:

> devtools::install_github("tidyverse/readr@922")
Downloading GitHub repo tidyverse/readr@922
✔  checking for file ‘/tmp/Rtmp00GCh4/remotes59694eb31c19/tidyverse-readr-da7e0bd/DESCRIPTION’ ...
   cp: cannot stat 'tidyverse-readr-da7e0bd/rcon': No such file or directory
    ERROR
   copying to build directory failed
Error in run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),  : 
  System command error

But this is on my computer at work (were I first noticed the problem and which started this issue), previous attempts of installing tidyverse/readr@922 were made on my computer at home. Theoretically they have the same set-up (in terms of R), but the former is still running Ubuntu 16.04 while my home computer is already running Ubuntu 18.04.

Other repositories can be installed with devtools::install_github() on my work computer, so it does not seem to be a firewall (or similar) issue.

@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 29, 2018

@jimhester I am back home now and on my home machine it works. So the problems that I experienced this morning must be due to something specific to my work machine (will have to look into that one myself, but I plan to upgrade that machine soon to Ubuntu 18.04 anyway, hopefully that will make the problem go away). Thank you for all your help and work on this.

> devtools::install_github("tidyverse/readr@922")
Downloading GitHub repo tidyverse/readr@922
✔  checking for file ‘/tmp/Rtmpb5Hlh3/remotesd97168acc9a/tidyverse-readr-9f6d3e3/DESCRIPTION’ ...
─  preparing ‘readr’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘readr_1.2.1.9000.tar.gz’
   
* installing *source* package ‘readr’ ...
** libs
*** arch - 32
g++ -m32  -I"/opt/R/R-3.5.1/lib/R/include" -I"/opt/R/R-3.5.1/lib/R/include/32" -DNDEBUG  -I"/home/opt/R/R-3.5.1/lib/R/library/Rcpp/include" -I"/home/opt/R/R-3.5.1/lib/R/library/BH/include" -I/usr/local/include  -I. -Ircon -fpic  -g -O2  -c Collector.cpp -o Collector.o
[...]
mkdir -p ../inst/rcon/64
g++  -shared -L"/opt/R/R-3.5.1/lib/R/lib/64" -L/usr/local/lib -o ../inst/rcon/64/librcon.so rcon/connection.o
g++ -shared -L/opt/R/R-3.5.1/lib/R/lib/64 -L/usr/local/lib -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o RcppExports.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o datetime.o grisu3.o init.o localtime.o parse.o read.o type_convert.o write.o write_connection.o write_delim.o -L. -lrcon -L../inst/rcon/64 -Wl,-rpath,$ORIGIN/../../rcon/64 -L/opt/R/R-3.5.1/lib/R/lib/64 -lR
installing via 'install.libs.R' to /home/opt/R/R-3.5.1/lib/R/library/readr
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - 32
*** arch - 64
* DONE (readr)

@jimhester
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@jimhester jimhester commented Nov 29, 2018

Ok, good to hear it now works! Thank you for your patience, I will likely release a new version of readr with these changes and those from #924 in the next few days.

@BerwinTurlach
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@BerwinTurlach BerwinTurlach commented Nov 29, 2018

@jimhester, well, I just ssh'd back into my office machine and started R from the command line. Now it seems to work there too. This morning I was working from withing RStudio. Could that IDE sabotage devtools::install_github()? :-)

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@jimhester jimhester commented Nov 29, 2018

The IDE sometimes does nefarious things, but in this case I think I just fixed the bug that was causing the build step to fail in 9f6d3e3

Glad to hear it is working on both machines!

@jimhester jimhester closed this in 1604275 Nov 29, 2018
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This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/

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