Can't find record-gcc-switches? What to do?

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1

Hello!

This occurs when I try to update R packages. The packages that need to be compiled like Rcpp etc. fail with an apparent gcc error:

g++: error: record-gcc-switches: No such file or directory

I don’t know what has gone wrong. If you need some additional info to help me out of this, I’ll submit that gladly.

Here’s full log of the update attempt and sessioInfo():

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/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/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/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

Cheers,

Antti

2

It should be given to the compiler as an option, perhaps the Makefile is missing -f in front of it, it should look like this; *-frecord-gcc-switches
*
In a nutshell; it’s a compiler option, not an application.

3

Thanks for help!

So how can I fix this? Should I suspect some broken package which I need to reinstall? Are you also suggesting to post this some other forum then?

Cheers!

4

When you say trying to compile. How? Using make?? if so something is wrong in the make file it is missing a -f in the compile line. .Without know exactly what youare doing and how you are trying to do it is is hard to give exact instructions

5

I let R do compiling. I just run update.packages() and let it do its job. Based on error message in log I was able to say that error happened during compiling. I’m complete novice in such matters and need help to interpret the message. However, I included the error message and told exactly what I did, so gogalthorp’s critique is dumb.

I guess I need to find someone who understands both R and openSUSE to help me with this. The problem persists.

6

You are compiling the R language I guess but it is written in c++ thus you must use c++ compilation and there is something wrong in the calls ie a -f is missing or there is an extra space. So what ever script you are using it is broken and must be repaired.

R-base is in the repos so you can install via yast just search for R-base

7

The problem persists even after 13.2 upgrade. So where to look next for a possible broken script?

8

In the package you are trying to install.

9

I finally solved it. A non-CRAN package rstan modified compiling instructions for Rcpp and apparently the version I had had an error. Reinstalling rstan solved the problem. Thanks all for help!