[R] Compilation error: Rcpp and related packages - record-gcc-switches missing

Antti Simola asimola78 at gmail.com
Wed Nov 12 16:20:40 CET 2014


Hello,

I encountered problem with Linux machine (openSUSE, 3.1.1. version of R)
while I tried to update the packages with update.packages(). Rcpp,
RcppArmadillo and RcppEigen refused to compile because record-gcc-swtiches
was missing. I don't know much about compiling and such so I didn't get any
further with the problem. Enquiries to Rcpp and openSUSE experts have not
solved my problem. What I learned was that -frecord-gcc-switches might be
mispelled somewhere. That information did not help me to find solution. If
anyone could help with this problem I would we very thankful. See the log
and SessionInfo() below for more detail:

Rcpp :
Version 0.11.2 installed in /home/antti/R/x86_64-suse-linux-gnu-library/3.1
Version 0.11.3 available at http://ftp.eenet.ee/pub/cran
Update (y/N/c)? y
RcppArmadillo :
Version 0.4.320.0 installed in
/home/antti/R/x86_64-suse-linux-gnu-library/3.1
Version 0.4.450.1.0 available at http://ftp.eenet.ee/pub/cran
Update (y/N/c)? y
RcppEigen :
Version 0.3.2.1.2 installed in
/home/antti/R/x86_64-suse-linux-gnu-library/3.1
Version 0.3.2.2.0 available at http://ftp.eenet.ee/pub/cran
Update (y/N/c)? y
trying URL 'http://ftp.eenet.ee/pub/cran/src/con..._0.11.3.tar.gz
<http://ftp.eenet.ee/pub/cran/src/contrib/Rcpp_0.11.3.tar.gz>'
Content type 'application/x-tar' length 2169583 bytes (2.1 Mb)
opened URL
==================================================
downloaded 2.1 Mb

trying URL 'http://ftp.eenet.ee/pub/cran/src/con...450.1.0.tar.gz
<http://ftp.eenet.ee/pub/cran/src/contrib/RcppArmadillo_0.4.450.1.0.tar.gz>'
Content type 'application/x-tar' length 931597 bytes (909 Kb)
opened URL
==================================================
downloaded 909 Kb

trying URL 'http://ftp.eenet.ee/pub/cran/src/con...3.2.2.0.tar.gz
<http://ftp.eenet.ee/pub/cran/src/contrib/RcppEigen_0.3.2.2.0.tar.gz>'
Content type 'application/x-tar' length 1216536 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/lib64/R/include -I../inst/include/ -I/usr/local/include -fpic
-fmessage-length=0 record-gcc-switches -fstack-protector -O3 -Wall
-D_FORTIFY_SOURCE=2 -funwind-tables -fasynchronous-unwind-tables -c
Date.cpp -o Date.o
g++: error: record-gcc-switches: No such file or directory
make: *** [Date.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/antti/R/x86_64-suse-linux-gnu-library/3.1/Rcpp’
* restoring previous ‘/home/antti/R/x86_64-suse-linux-gnu-library/3.1/Rcpp’
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
* checking LAPACK_LIBS: divide-and-conquer complex SVD available via
R-supplied LAPACK
** libs
g++ -I/usr/lib64/R/include -I/usr/local/include
-I"/home/antti/R/x86_64-suse-linux-gnu-library/3.1/Rcpp/include"
-I../inst/include -fpic -fmessage-length=0 record-gcc-switches
-fstack-protector -O3 -Wall -D_FORTIFY_SOURCE=2 -funwind-tables
-fasynchronous-unwind-tables -c RcppArmadillo.cpp -o RcppArmadillo.o
g++: error: record-gcc-switches: No such file or directory
make: *** [RcppArmadillo.o] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/home/antti/R/x86_64-suse-linux-gnu-library/3.1/RcppArmadillo’
* restoring previous
‘/home/antti/R/x86_64-suse-linux-gnu-library/3.1/RcppArmadillo’
* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/lib64/R/include -I/usr/local/include
-I"/home/antti/R/x86_64-suse-linux-gnu-library/3.1/Rcpp/include"
-I../inst/include -fpic -fmessage-length=0 record-gcc-switches
-fstack-protector -O3 -Wall -D_FORTIFY_SOURCE=2 -funwind-tables
-fasynchronous-unwind-tables -c RcppEigen.cpp -o RcppEigen.o
g++: error: record-gcc-switches: No such file or directory
make: *** [RcppEigen.o] Error 1
ERROR: compilation failed for package ‘RcppEigen’
* removing ‘/home/antti/R/x86_64-suse-linux-gnu-library/3.1/RcppEigen’
* restoring previous
‘/home/antti/R/x86_64-suse-linux-gnu-library/3.1/RcppEigen’

The downloaded source packages are in
‘/tmp/Rtmpnx5dfE/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package ‘Rcpp’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package ‘RcppArmadillo’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl, :
installation of package ‘RcppEigen’ had non-zero exit status
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-suse-linux-gnu (64-bit)

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

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

loaded via a namespace (and not attached):
[1] compiler_3.1.1 tcltk_3.1.1 tools_3.1.1

Cheer,

Antti

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