I don't know if this is a bug, or I am missing something in my system. Any help appreciated

Thanks Matt Shenton

renv::install("bioc::gpart")

Installing graph [1.72.0] ...
    OK [built from source]
Moving graph [1.72.0] into the cache ...
    OK [moved to cache in 0.18 milliseconds]
Installing RBGL [1.70.0] ...
    OK [built from source]
Moving RBGL [1.70.0] into the cache ...
    OK [moved to cache in 0.18 milliseconds]
Installing OrganismDbi [1.36.0] ...
    OK [built from source]
Moving OrganismDbi [1.36.0] into the cache ...
    OK [moved to cache in 0.19 milliseconds]
Installing GO.db [3.14.0] ...
    OK [built from source]
Moving GO.db [3.14.0] into the cache ...
    OK [moved to cache in 0.44 milliseconds]
Installing org.Hs.eg.db [3.14.0] ...
    OK [built from source]
Moving org.Hs.eg.db [3.14.0] into the cache ...
    OK [moved to cache in 0.18 milliseconds]
Installing TxDb.Hsapiens.UCSC.hg19.knownGene [3.2.2] ...
    OK [built from source]
Moving TxDb.Hsapiens.UCSC.hg19.knownGene [3.2.2] into the cache ...
    OK [moved to cache in 0.3 milliseconds]
Installing Homo.sapiens [1.3.1] ...
    OK [built from source]
Moving Homo.sapiens [1.3.1] into the cache ...
    OK [moved to cache in 0.19 milliseconds]
Installing TxDb.Hsapiens.UCSC.hg38.knownGene [3.14.0] ...
    OK [built from source]
Moving TxDb.Hsapiens.UCSC.hg38.knownGene [3.14.0] into the cache ...
    OK [moved to cache in 0.18 milliseconds]

Installing gpart [1.12.0] ...
    FAILED
Error installing package 'gpart':
=================================

* installing to library ‘/home/mshenton/analysis/LDblocks/renv/staging/1’
* installing *source* package ‘gpart’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mshenton/analysis/LDblocks/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mshenton/analysis/LDblocks/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gpart_cpp.cpp -o gpart_cpp.o
gpart_cpp.cpp: In function ‘uint32_t cubic_real_roots(double, double, double, Rcpp::NumericVector)’:
gpart_cpp.cpp:622:42: error: ‘PI’ was not declared in this scope
  622 |     solutions[1] = sq * cos(dxx + (2.0 * PI / 3.0)) - adiv3;
      |                                          ^~
make: *** [/usr/lib/R/etc/Makeconf:177: gpart_cpp.o] Error 1
ERROR: compilation failed for package ‘gpart’
* removing ‘/home/mshenton/analysis/LDblocks/renv/staging/1/gpart’
Error: install of package 'gpart' failed [error code 1]

Try the following:

Download and unpack the source code to a directory on your computer first, say mydir/gpart.

Then add the line to the file part_cpp.cpp in subdirectory src:

define PI 3.141593

This can be done near all the other #define lines at the top of the file. You can add digits if you want a more precise PI.

Finally, install the package from this modified version using install.packages("mydir/gpart", repos = NULL, type = "source")

Best, Bert Klei Computational Genetics WPH-UPMC