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Installing readODS from CRAN failed :write_sheet_file_.cpp:158:21: error: invalid use of incomplete type ‘struct SEXPREC’ #174
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> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora Linux 38 (Workstation Edition)
Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1
> |
Thank you very much! The most immediate thing that I can do is to use rhub's Fedora instance to check the package. https://builder.r-hub.io/status/original/readODS_2.1.1.tar.gz-5a4bad741cdb412a94c50f4f86e2c5e1 And it returned okay. I was wondering whether it is a general issue in your Fedora setup with compiling packages using |
It's ok to install > install.packages("readxl", dependencies = T)
Installing package into ‘/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/readxl_1.4.3.tar.gz'
Content type 'application/octet-stream' length 2093488 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
* installing *source* package ‘readxl’ ...
** package ‘readxl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 13.2.1 20230728 (Red Hat 13.2.1-1)’
using C++ compiler: ‘g++ (GCC) 13.2.1 20230728 (Red Hat 13.2.1-1)’
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c XlsWorkBook.cpp -o XlsWorkBook.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c XlsxWorkBook.cpp -o XlsxWorkBook.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c zip.cpp -o zip.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Read.cpp -o Read.o
gcc -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c cran.c -o cran.o
gcc -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c libxls/xlstool.c -o libxls/xlstool.o
gcc -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c libxls/endian.c -o libxls/endian.o
gcc -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c libxls/ole.c -o libxls/ole.o
gcc -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c libxls/xls.c -o libxls/xls.o
gcc -I"/usr/include/R" -DNDEBUG -Iunix -I. -I'/usr/share/R/library/cpp11/include' -I'/home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c libxls/locale.c -o libxls/locale.o
g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o readxl.so cpp11.o XlsWorkBook.o XlsxWorkBook.o zip.o Read.o cran.o libxls/xlstool.o libxls/endian.o libxls/ole.o libxls/xls.o libxls/locale.o -L/usr/lib64/R/lib -lR
installing to /home/xibo/R/x86_64-redhat-linux-gnu-library/4.3/00LOCK-readxl/00new/readxl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘readxl’
finding HTML links ... done
cell-specification html
finding level-2 HTML links ... done
excel_format html
excel_sheets html
read_excel html
readxl-package html
readxl_example html
readxl_progress html
*** copying figures
** 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 (readxl)
The downloaded source packages are in
‘/tmp/RtmpUodOb4/downloaded_packages’
> |
Thank you very much again. I have tried this locally (But i must admit that I am no expert in Fedora). docker run --rm -it fedora And then inside the container dnf install R -y ; Rscript -e "install.packages('readODS', repo = 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/')"
Of course, no computational environment is 100% the same. And I don't know how different is your current computational environment to the one bootstrapped by Docker. So, it probably won't help. Could you please also try the following and report:
If both still do not work, I think there are some precautionary steps I can take to "prevent" this, e.g. readODS/src/write_sheet_file_.cpp Lines 157 to 159 in 7548c3a
To for (int i = 0; i < sheet_names.size(); i++) {
cpp11::data_frame current_df;
write_df(current_df, sheet_names[i], row_names, col_names, na_as_string, padding, xml_file);
} But this problem should have been fixed since a decade. |
The error messages as follows:
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