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R install.packages polyclip: where is config.log? No answer in prior posts
Asked Answered
rg++install.packagesggforce
N

1

5

Attempting to install R package ggforce encountered following error installing dependency polyclip which referred me to config.log. However, config.log is not found below ~/, /tmp, or /var/log I checked this via

find . | grep config[.]log

Tried install.packages("ggforce",keep_outputs = TRUE) which did not provide any additional information;

 install.packages("ggforce",keep_outputs = TRUE,verbose = TRUE)

"configure: error: in `/tmp/RtmpAkq4Vm/R.INSTALL6c31457f19ba/polyclip'"

however /tmp/RtmpAkq4Vm did not exist post installation.

Can somebody tell me where it is?

Error detail:

 install.packages("ggforce")
Installing package into ‘/home/dutky/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependency ‘polyclip’

trying URL 'https://cloud.r-project.org/src/contrib/polyclip_1.10-0.tar.gz'
Content type 'application/x-gzip' length 79619 bytes (77 KB)
==================================================
downloaded 77 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggforce_0.3.1.tar.gz'
Content type 'application/x-gzip' length 857814 bytes (837 KB)
==================================================
downloaded 837 KB

[1] "sourcing Rprofile.site"
* installing *source* package ‘polyclip’ ...
** package ‘polyclip’ successfully unpacked and MD5 sums checked
** using staged installation
compiling under C++11
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpCWyOfl/R.INSTALL3a4b31b841d7/polyclip':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘polyclip’
* removing ‘/home/dutky/R/x86_64-pc-linux-gnu-library/3.6/polyclip’
Warning in install.packages :
  installation of package ‘polyclip’ had non-zero exit status
[1] "sourcing Rprofile.site"
ERROR: dependency ‘polyclip’ is not available for package ‘ggforce’
* removing ‘/home/dutky/R/x86_64-pc-linux-gnu-library/3.6/ggforce’
Warning in install.packages :
  installation of package ‘ggforce’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpTKDy0n/downloaded_packages’

Running ubuntu 16.04.12, 64 bit, gcc/g++:

dutky@stillbill:/var/log$ g++ --version
g++ (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

dutky@stillbill:/var/log$ gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Nakitanalani answered 7/12, 2019 at 19:9 Comment(2)
Do you have C++11? – Salisbarry
See above: there is no config.out left in /tmp c++ starts a chain of links resolving to /usr/bin/g++-5 – Nakitanalani
N
6

Installing package polyclip choked on something in my .Rprofile. I moved it out of the way and the ggforce install completed successfully.

I got a link to the config.log file during installation before it presumably got deleted by sourcing the following in another bash shell:

while true ; do
    if [  -e config.log ]
        then return
    fi
    save=`find /tmp -name config.log -exec ln {} config.log \;` 
done 2>/dev/null

config.log contained the following after the error occurred:

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by polyclip configure 1.9-1, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure 

## --------- ##
## Platform. ##
## --------- ##

hostname = stillbill
uname -m = x86_64
uname -r = 4.15.0-72-generic
uname -s = Linux
uname -v = #81~16.04.1-Ubuntu SMP Tue Nov 26 16:34:21 UTC 2019

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /home/dutky/bin
PATH: /home/dutky/.local/bin
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /usr/local/games
PATH: /snap/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2065: checking for C++ compiler version
configure:2074: ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11' ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11STD' --version >&5
./configure: line 2076: ERROR:: command not found
configure:2085: $? = 127
configure:2074: ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11' ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11STD' -v >&5
./configure: line 2076: ERROR:: command not found
configure:2085: $? = 127
configure:2074: ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11' ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11STD' -V >&5
./configure: line 2076: ERROR:: command not found
configure:2085: $? = 127
configure:2074: ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11' ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11STD' -qversion >&5
./configure: line 2076: ERROR:: command not found
configure:2085: $? = 127
configure:2105: checking whether the C++ compiler works
configure:2127: ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11' ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11STD' ERROR: no information for variable '[1] "sourcing Rprofile.site"
CXX11FLAGS'   conftest.cpp  >&5
./configure: line 2129: ERROR:: command not found
configure:2131: $? = 127
configure:2169: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "polyclip"
| #define PACKAGE_TARNAME "polyclip"
| #define PACKAGE_VERSION "1.9-1"
| #define PACKAGE_STRING "polyclip 1.9-1"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| 
|   ;
|   return 0;
| }
configure:2174: error: in `/tmp/RtmpQ1YEV6/R.INSTALL6897499f5a39/polyclip':
configure:2176: error: C++ compiler cannot create executables
See `config.log' for more details

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=

## ----------------- ##
## Output variables. ##
## ----------------- ##

CPPFLAGS=''
CXX11'\'' ERROR: no information for variable '\''[1] "sourcing Rprofile.site"
CXX11FLAGS'\'''
CXX11STD'\'''
CXX='ERROR: no information for variable '\''[1] "sourcing Rprofile.site"
CXXCPP=''
CXXFLAGS='ERROR: no information for variable '\''[1] "sourcing Rprofile.site"
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
GREP=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
OBJEXT=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME='polyclip'
PACKAGE_STRING='polyclip 1.9-1'
PACKAGE_TARNAME='polyclip'
PACKAGE_URL=''
PACKAGE_VERSION='1.9-1'
PATH_SEPARATOR=':'
POLYCLIP_CPPFLAGS=''
POLYCLIP_CXXFLAGS=''
POLYCLIP_CXX_DECLAR='CXX_STD = CXX11'
POLYCLIP_LIBS=''
POLYCLIP_OBJECTS=''
SHELL='/bin/bash'
ac_ct_CXX=''
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "polyclip"
#define PACKAGE_TARNAME "polyclip"
#define PACKAGE_VERSION "1.9-1"
#define PACKAGE_STRING "polyclip 1.9-1"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""

configure: exit 77
$
Nakitanalani answered 7/12, 2019 at 23:11 Comment(1)
Same problem; same solution (temporarily removed Rprofile). – Sixtyfourmo

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