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cannot be installed with `devtools::install_github('quantling/ndl2') #1

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derNarr opened this issue Nov 24, 2022 · 0 comments
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@derNarr
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derNarr commented Nov 24, 2022

For some reason it is not possible to install ndl2 with `devtools:install_github('quantling/ndl2').

After installing devtools and the dependencies of ndl2 with:

sudo apt-get install r-cran-devtools
sudo apt-get install libboost-filesystem-dev libboost-system-dev libboost-regex-dev libicu-dev

I still get an error message after running:

library(devtools)
devtools::install_github('quantling/ndl2')

The error message is:

Downloading GitHub repo quantling/ndl2@HEAD
✔  checking for file ‘/tmp/RtmpFbrjVv/remotes1f67548ee37a1/quantling-ndl2-5f26ad0/DESCRIPTION’ ...
─  preparing ‘ndl2’:
✔  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 ‘ndl2_0.1.1.tar.gz’
   
Installing package into ‘/home/tino/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package ‘ndl2’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c common/helper.cpp -o common/helper.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c common/serialization.cpp -o common/serialization.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c common/Exception.cpp -o common/Exception.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c common/view_events.cpp -o common/view_events.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c danks.cpp -o danks.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c learning/rescorla_wagner.cpp -o learning/rescorla_wagner.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c learning/file_management.cpp -o learning/file_management.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c learning/util.cpp -o learning/util.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c learning/matrix_io.cpp -o learning/matrix_io.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c learning/events_manager.cpp -o learning/events_manager.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c learning/r_wrapper.cpp -o learning/r_wrapper.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c preprocessing/ndlpreproc.cpp -o preprocessing/ndlpreproc.o
preprocessing/ndlpreproc.cpp: In function ‘std::string getFormattedTime(tm*)’:
preprocessing/ndlpreproc.cpp:1539:31: warning: ‘%02d’ directive output may be truncated writing between 2 and 11 bytes into a region of size between 8 and 15 [-Wformat-truncation=]
 1539 |     snprintf(buffer, 20, "%4d-%02d-%02d %02d:%02d:%02d", 1900+ptm->tm_year,
      |                               ^~~~
preprocessing/ndlpreproc.cpp:1539:26: note: directive argument in the range [-2147483647, 2147483647]
 1539 |     snprintf(buffer, 20, "%4d-%02d-%02d %02d:%02d:%02d", 1900+ptm->tm_year,
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from /usr/include/c++/10/cstdio:42,
                 from preprocessing/ndlpreproc.cpp:10:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 20 and 72 bytes into a destination of size 20
   67 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   68 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c preprocessing/ndlOutBuffer.cpp -o preprocessing/ndlOutBuffer.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c view_events_wrapper.cpp -o view_events_wrapper.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tino/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fopenmp -DUSING_RCPP=1 -Wall -fpic  -g -O2 -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c preprocessing_wrapper.cpp -o preprocessing_wrapper.o
make: *** No rule to make target 'RcppExports.o', needed by 'ndl2.so'.  Stop.
ERROR: compilation failed for package ‘ndl2’
* removing ‘/home/tino/R/x86_64-pc-linux-gnu-library/4.2/ndl2’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpFbrjVv/file1f675655196fa/ndl2_0.1.1.tar.gz’ had non-zero exit status
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