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unable to install teachingApps 1.0.4 #12

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iembry opened this issue Jul 30, 2019 · 7 comments
Open

unable to install teachingApps 1.0.4 #12

iembry opened this issue Jul 30, 2019 · 7 comments

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@iembry
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iembry commented Jul 30, 2019

Hi, I am unable to install teachingApps version 1.0.4. I have included some system information below:

CRAN (R 3.6.1)
GNU/Linux Trisquel distribution (Ubuntu14.04)
BH 1.69.0-1 2019-01-07
g++ 4.8.4

The following is the installation log:

   * installing *source* package ‘teachingApps’ ...
** package ‘teachingApps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
ccache g++ -std=c++11 -I"/usr/share/R/include" -DNDEBUG  -I"/library/Rcpp/include" -I"/library/BH/include" -I"/library/RcppEigen/include" -I"/library/RcppNumerical/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
ccache g++ -std=c++11 -I"/usr/share/R/include" -DNDEBUG  -I"/library/Rcpp/include" -I"/library/BH/include" -I"/library/RcppEigen/include" -I"/library/RcppNumerical/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c beta_funcs.cpp -o beta_funcs.o
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/pending/integer_log2.hpp:7:2: error: stray ‘#’ in program
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
  ^
line-map.c: file "/library/BH/include/boost/random/detail/large_arithmetic.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/large_arithmetic.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/large_arithmetic.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/const_mod.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/const_mod.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/const_mod.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "beta_funcs.cpp" left but not entered
line-map.c: file "beta_funcs.cpp" left but not entered
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/pending/integer_log2.hpp:7:97: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                                 ^
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/pending/integer_log2.hpp:7:4: error: expected unqualified-id before numeric constant
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
    ^
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:21:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/random/detail/disable_warnings.hpp:27:28: error: expected declaration before end of line
 #pragma GCC diagnostic push
                            ^
make: *** [beta_funcs.o] Error 1
ERROR: compilation failed for package ‘teachingApps’
* removing ‘/library/teachingApps’
* restoring previous ‘/library/teachingApps’
@Auburngrads
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Thanks for including the install log.

Looks like an issue with boost via BH, but I'll look through beta_funcs to see if I can circumvent the pragma error.

@iembry
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iembry commented Aug 1, 2019 •
edited
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@Auburngrads You're welcome for the install log.

This is my system information:

CRAN (R 3.6.1)
Trisquel 7.0 GNU/Linux distribution (Ubuntu 14.04)
BH 1.69.0-1 2019-01-07
g++ 4.8.4

Thank you.

@Auburngrads
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Owner

I assume you are attempting to install from CRAN, not github - is this correct?

So, far I can't replicate your error. On Windows I see a note about the deprecated boost header, but no error.

I also used rhub to check on ubuntu, and saw no errors there either.

I'll keep looking

@iembry
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iembry commented Aug 2, 2019

@Auburngrads Yes, I was attempting to install from CRAN. Maybe it has to do with the older (< 4.9) version of gcc that I am using. I have had similar issues with other R packages too. Thank you.

@Auburngrads
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Owner

The fact that this is happening for you when attempting to install multiple packages makes me think the issue may not be with teachingApps.

Do you have any installation issues that are specific to this package?

@iembry
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iembry commented Aug 9, 2019

Hi, I have re-installed teachingApps by itself to show that the error was with that package rather than other ones.

Thank you.

Please see below:

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("teachingApps") 
Installing package into ‘/library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/teachingApps_1.0.4.tar.gz'
Content type 'application/x-gzip' length 621571 bytes (607 KB)
==================================================
downloaded 607 KB

* installing *source* package ‘teachingApps’ ...
** package ‘teachingApps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
ccache g++ -std=c++11 -I"/usr/share/R/include" -DNDEBUG  -I"/library/Rcpp/include" -I"/library/BH/include" -I"/library/RcppEigen/include" -I"/library/RcppNumerical/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
ccache g++ -std=c++11 -I"/usr/share/R/include" -DNDEBUG  -I"/library/Rcpp/include" -I"/library/BH/include" -I"/library/RcppEigen/include" -I"/library/RcppNumerical/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c beta_funcs.cpp -o beta_funcs.o
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/pending/integer_log2.hpp:7:2: error: stray ‘#’ in program
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
  ^
line-map.c: file "/library/BH/include/boost/random/detail/large_arithmetic.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/large_arithmetic.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/large_arithmetic.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/const_mod.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/const_mod.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/const_mod.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/detail/seed_impl.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "/library/BH/include/boost/random/mersenne_twister.hpp" left but not entered
line-map.c: file "beta_funcs.cpp" left but not entered
line-map.c: file "beta_funcs.cpp" left but not entered
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/pending/integer_log2.hpp:7:97: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                                 ^
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/pending/integer_log2.hpp:7:4: error: expected unqualified-id before numeric constant
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
    ^
In file included from /library/BH/include/boost/random/detail/integer_log2.hpp:21:0,
                 from /library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from beta_funcs.cpp:9:
/library/BH/include/boost/random/detail/disable_warnings.hpp:27:28: error: expected declaration before end of line
 #pragma GCC diagnostic push
                            ^
make: *** [beta_funcs.o] Error 1
ERROR: compilation failed for package ‘teachingApps’
* removing ‘/library/teachingApps’
* restoring previous ‘/library/teachingApps’

The downloaded source packages are in
        ‘/tmp/RtmpnR9osC/downloaded_packages’
Warning message:
In install.packages("teachingApps") :
  installation of package ‘teachingApps’ had non-zero exit status

@Auburngrads
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This is not what I meant.

You previously said that you get similar installation errors when installing other packages.

Is this still the case or is teachingApps the only package for which this happens?

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@Auburngrads @iembry