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bnosac / crfsuite

Labelling Sequential Data in Natural Language Processing with R - using CRFsuite
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crf/src/crf1d_model.c:127:12: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=] #14

Closed mattdowle closed 3 years ago

mattdowle commented 3 years ago

Hi, Thanks for using data.table. In revdep testing for the next release, I'm seeing the following compiler warning for crfsuite. I see everything is fully OK on CRAN, though. I have just upgraded to gcc 10.2.0 so maybe that's why. I'm surprised though as usually CRAN is the first to use latest compilers and spot things like this first. Best, Matt

* installing *source* package ‘crfsuite’ ...
** package ‘crfsuite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c cqdb/src/cqdb.c -o cqdb/src/cqdb.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c cqdb/src/lookup3.c -o cqdb/src/lookup3.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c liblbfgs/lib/lbfgs.c -o liblbfgs/lib/lbfgs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_context.c -o crf/src/crf1d_context.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_encode.c -o crf/src/crf1d_encode.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_feature.c -o crf/src/crf1d_feature.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_model.c -o crf/src/crf1d_model.o
In function ‘read_uint8_array’,
    inlined from ‘crf1dm_new_impl’ at crf/src/crf1d_model.c:735:10:
crf/src/crf1d_model.c:127:12: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=]
  127 |     *value = *buffer;
      |     ~~~~~~~^~~~~~~~~
crf/src/crf1d_model.c: In function ‘crf1dm_new_impl’:
crf/src/crf1d_model.c:64:17: note: at offset 0 to object ‘magic’ with size 4 declared here
   64 |     uint8_t     magic[4];       /* File magic. */
      |                 ^~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_tag.c -o crf/src/crf1d_tag.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crfsuite.c -o crf/src/crfsuite.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crfsuite_train.c -o crf/src/crfsuite_train.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/dataset.c -o crf/src/dataset.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/dictionary.c -o crf/src/dictionary.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/holdout.c -o crf/src/holdout.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/logging.c -o crf/src/logging.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/params.c -o crf/src/params.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/quark.c -o crf/src/quark.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/rumavl.c -o crf/src/rumavl.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_arow.c -o crf/src/train_arow.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_averaged_perceptron.c -o crf/src/train_averaged_perceptron.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_l2sgd.c -o crf/src/train_l2sgd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_lbfgs.c -o crf/src/train_lbfgs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_passive_aggressive.c -o crf/src/train_passive_aggressive.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rcpp_crfsuite.cpp -o rcpp_crfsuite.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o crfsuite.so cqdb/src/cqdb.o cqdb/src/lookup3.o liblbfgs/lib/lbfgs.o crf/src/crf1d_context.o crf/src/crf1d_encode.o crf/src/crf1d_feature.o crf/src/crf1d_model.o crf/src/crf1d_tag.o crf/src/crfsuite.o crf/src/crfsuite_train.o crf/src/dataset.o crf/src/dictionary.o crf/src/holdout.o crf/src/logging.o crf/src/params.o crf/src/quark.o crf/src/rumavl.o crf/src/train_arow.o crf/src/train_averaged_perceptron.o crf/src/train_l2sgd.o crf/src/train_lbfgs.o crf/src/train_passive_aggressive.o rcpp_crfsuite.o RcppExports.o -L/usr/lib/R/lib -lR
rm -f cqdb/src/cqdb.o cqdb/src/lookup3.o liblbfgs/lib/lbfgs.o crf/src/crf1d_context.o crf/src/crf1d_encode.o crf/src/crf1d_feature.o crf/src/crf1d_model.o crf/src/crf1d_tag.o crf/src/crfsuite.o crf/src/crfsuite_train.o crf/src/dataset.o crf/src/dictionary.o crf/src/holdout.o crf/src/logging.o crf/src/params.o crf/src/quark.o crf/src/rumavl.o crf/src/train_arow.o crf/src/train_averaged_perceptron.o crf/src/train_l2sgd.o crf/src/train_lbfgs.o crf/src/train_passive_aggressive.o rcpp_crfsuite.o RcppExports.o 
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c cqdb/src/cqdb.c -o cqdb/src/cqdb.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c cqdb/src/lookup3.c -o cqdb/src/lookup3.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c liblbfgs/lib/lbfgs.c -o liblbfgs/lib/lbfgs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_context.c -o crf/src/crf1d_context.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_encode.c -o crf/src/crf1d_encode.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_feature.c -o crf/src/crf1d_feature.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_model.c -o crf/src/crf1d_model.o
In function ‘read_uint8_array’,
    inlined from ‘crf1dm_new_impl’ at crf/src/crf1d_model.c:735:10:
crf/src/crf1d_model.c:127:12: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=]
  127 |     *value = *buffer;
      |     ~~~~~~~^~~~~~~~~
crf/src/crf1d_model.c: In function ‘crf1dm_new_impl’:
crf/src/crf1d_model.c:64:17: note: at offset 0 to object ‘magic’ with size 4 declared here
   64 |     uint8_t     magic[4];       /* File magic. */
      |                 ^~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crf1d_tag.c -o crf/src/crf1d_tag.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crfsuite.c -o crf/src/crfsuite.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/crfsuite_train.c -o crf/src/crfsuite_train.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/dataset.c -o crf/src/dataset.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/dictionary.c -o crf/src/dictionary.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/holdout.c -o crf/src/holdout.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/logging.c -o crf/src/logging.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/params.c -o crf/src/params.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/quark.c -o crf/src/quark.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/rumavl.c -o crf/src/rumavl.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_arow.c -o crf/src/train_arow.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_averaged_perceptron.c -o crf/src/train_averaged_perceptron.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_l2sgd.c -o crf/src/train_l2sgd.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_lbfgs.c -o crf/src/train_lbfgs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -O3 -c crf/src/train_passive_aggressive.c -o crf/src/train_passive_aggressive.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rcpp_crfsuite.cpp -o rcpp_crfsuite.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./cqdb/include -I./crf/src -I./liblbfgs/include -I./include -I'/home/mdowle/build/revdeplib/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
installing to /home/mdowle/build/revdeplib/crfsuite.Rcheck/00LOCK-crfsuite/00new/crfsuite/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (crfsuite)
$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 10.2.0-13ubuntu1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 10.2.0 (Ubuntu 10.2.0-13ubuntu1) 
crfsuite_0.3.4.tar.gz
./crfsuite.Rcheck/00check.log:* using log directory ‘/home/mdowle/build/revdeplib/crfsuite.Rcheck’
./crfsuite.Rcheck/00check.log:* using R version 4.0.3 (2020-10-10)
./crfsuite.Rcheck/00check.log:* using platform: x86_64-pc-linux-gnu (64-bit)
./crfsuite.Rcheck/00check.log:* using session charset: UTF-8
./crfsuite.Rcheck/00check.log:* checking for file ‘crfsuite/DESCRIPTION’ ... OK
./crfsuite.Rcheck/00check.log:* checking extension type ... Package
./crfsuite.Rcheck/00check.log:* this is package ‘crfsuite’ version ‘0.3.4’
./crfsuite.Rcheck/00check.log:* checking package namespace information ... OK
./crfsuite.Rcheck/00check.log:* checking package dependencies ... OK
./crfsuite.Rcheck/00check.log:* checking if this is a source package ... OK
./crfsuite.Rcheck/00check.log:* checking if there is a namespace ... OK
./crfsuite.Rcheck/00check.log:* checking for executable files ... OK
./crfsuite.Rcheck/00check.log:* checking for hidden files and directories ... OK
./crfsuite.Rcheck/00check.log:* checking for portable file names ... OK
./crfsuite.Rcheck/00check.log:* checking for sufficient/correct file permissions ... OK
./crfsuite.Rcheck/00check.log:* checking whether package ‘crfsuite’ can be installed ... WARNING
./crfsuite.Rcheck/00check.log:Found the following significant warnings:
./crfsuite.Rcheck/00check.log:  crf/src/crf1d_model.c:127:12: warning: writing 16 bytes into a region of size 4 [-Wstringop-overflow=]
./crfsuite.Rcheck/00check.log:See ‘/home/mdowle/build/revdeplib/crfsuite.Rcheck/00install.out’ for details.
./crfsuite.Rcheck/00check.log:* checking installed package size ... OK
./crfsuite.Rcheck/00check.log:* checking package directory ... OK
./crfsuite.Rcheck/00check.log:* checking ‘build’ directory ... OK
./crfsuite.Rcheck/00check.log:* checking DESCRIPTION meta-information ... OK
./crfsuite.Rcheck/00check.log:* checking top-level files ... OK
./crfsuite.Rcheck/00check.log:* checking for left-over files ... OK
./crfsuite.Rcheck/00check.log:* checking index information ... OK
./crfsuite.Rcheck/00check.log:* checking package subdirectories ... OK
./crfsuite.Rcheck/00check.log:* checking R files for non-ASCII characters ... OK
./crfsuite.Rcheck/00check.log:* checking R files for syntax errors ... OK
./crfsuite.Rcheck/00check.log:* checking whether the package can be loaded ... OK
./crfsuite.Rcheck/00check.log:* checking whether the package can be loaded with stated dependencies ... OK
./crfsuite.Rcheck/00check.log:* checking whether the package can be unloaded cleanly ... OK
./crfsuite.Rcheck/00check.log:* checking whether the namespace can be loaded with stated dependencies ... OK
./crfsuite.Rcheck/00check.log:* checking whether the namespace can be unloaded cleanly ... OK
./crfsuite.Rcheck/00check.log:* checking loading without being on the library search path ... OK
./crfsuite.Rcheck/00check.log:* checking dependencies in R code ... OK
./crfsuite.Rcheck/00check.log:* checking S3 generic/method consistency ... OK
./crfsuite.Rcheck/00check.log:* checking replacement functions ... OK
./crfsuite.Rcheck/00check.log:* checking foreign function calls ... OK
./crfsuite.Rcheck/00check.log:* checking R code for possible problems ... OK
./crfsuite.Rcheck/00check.log:* checking Rd files ... OK
./crfsuite.Rcheck/00check.log:* checking Rd metadata ... OK
./crfsuite.Rcheck/00check.log:* checking Rd cross-references ... OK
./crfsuite.Rcheck/00check.log:* checking for missing documentation entries ... OK
./crfsuite.Rcheck/00check.log:* checking for code/documentation mismatches ... OK
./crfsuite.Rcheck/00check.log:* checking Rd \usage sections ... OK
./crfsuite.Rcheck/00check.log:* checking Rd contents ... OK
./crfsuite.Rcheck/00check.log:* checking for unstated dependencies in examples ... OK
./crfsuite.Rcheck/00check.log:* checking contents of ‘data’ directory ... OK
./crfsuite.Rcheck/00check.log:* checking data for non-ASCII characters ... OK
./crfsuite.Rcheck/00check.log:* checking data for ASCII and uncompressed saves ... OK
./crfsuite.Rcheck/00check.log:* checking line endings in C/C++/Fortran sources/headers ... OK
./crfsuite.Rcheck/00check.log:* checking line endings in Makefiles ... OK
./crfsuite.Rcheck/00check.log:* checking compilation flags in Makevars ... OK
./crfsuite.Rcheck/00check.log:* checking for GNU extensions in Makefiles ... OK
./crfsuite.Rcheck/00check.log:* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
./crfsuite.Rcheck/00check.log:* checking use of PKG_*FLAGS in Makefiles ... OK
./crfsuite.Rcheck/00check.log:* checking compiled code ... OK
./crfsuite.Rcheck/00check.log:* checking installed files from ‘inst/doc’ ... OK
./crfsuite.Rcheck/00check.log:* checking files in ‘vignettes’ ... OK
./crfsuite.Rcheck/00check.log:* checking examples ... OK
./crfsuite.Rcheck/00check.log:* checking for unstated dependencies in vignettes ... OK
./crfsuite.Rcheck/00check.log:* checking package vignettes in ‘inst/doc’ ... OK
./crfsuite.Rcheck/00check.log:* checking running R code from vignettes ... NONE
./crfsuite.Rcheck/00check.log:  ‘crfsuite-nlp.Rmd’ using ‘UTF-8’... OK
./crfsuite.Rcheck/00check.log:* checking re-building of vignette outputs ... OK
./crfsuite.Rcheck/00check.log:* checking PDF version of manual ... OK
./crfsuite.Rcheck/00check.log:* DONE
./crfsuite.Rcheck/00check.log:Status: 1 WARNING
jwijffels commented 3 years ago

Hi Matt. Thanks for the service. Wasn't aware of this -Wstringop-overflow= Is this holding you back from releasing data.table to CRAN?

jwijffels commented 3 years ago

And Matt, just wanted to let you know data.table is GREAT! And many thanks for the efforts on that package.

mattdowle commented 3 years ago

Sure thing. Thanks. No it's not holding the release up.

mattdowle commented 3 years ago

A similar problem with another package (Rgraphviz) was solved by using -O2 instead of -O3. So I tried that for crfsuite too, and lucky me, it worked. I did look at the line of code in your package, and it's only 2 lines in that function :

static int read_uint8(const uint8_t* buffer, uint8_t* value)
{
    *value = *buffer;   // line 127
    return sizeof(*value);
}

For the life of me, that looks fine to me. I can't see how there could ever be an overflow with that simple assign and that function signature.

So, since R CMD check crfsuite_0.3.4.tar.gz passes flawlessly with -O2, I'd put it down to a possible problem in the compiler with -O3.

$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 10.2.0-13ubuntu1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-JvwpWM/gcc-10-10.2.0/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 10.2.0 (Ubuntu 10.2.0-13ubuntu1)
jwijffels commented 3 years ago

Thanks for the doing the code inspection and providing your C expert knowledge.