data.table fails to be built on PowerPC with gcc7

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
r

Research direction

Reproduce the source installation on the reported R 4.1.2, PowerPC, OS X 10.6 environment and inspect the final data_table.so install step involving install_name_tool. Compare the generated object and build output with a working platform; done means data.table installs successfully without the malformed-object error.

Written by the indexing model from the issue text.

Description

install platform-specific

I am trying to install the package with R 4.1.2 running on 10.6 PowerPC, and it fails to compile. MacPorts gcc7 compiler is set (the latest confirmed to be working as of now).

`> install.packages("data.table", type = "source",

Warning in file(con, "r") :
  cannot open file '/var/db/timezone/zoneinfo/+VERSION': No such file or directory

  • installing source package ‘data.table’ ...
    ** using staged installation
    zlib 1.2.11 is available ok
    R CMD SHLIB supports OpenMP without any extra hint
    ** libs
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c assign.c -o assign.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c between.c -o between.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c bmerge.c -o bmerge.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c chmatch.c -o chmatch.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c cj.c -o cj.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c coalesce.c -o coalesce.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c dogroups.c -o dogroups.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fastmean.c -o fastmean.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fcast.c -o fcast.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fifelse.c -o fifelse.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fmelt.c -o fmelt.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c forder.c -o forder.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c frank.c -o frank.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fread.c -o fread.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c freadR.c -o freadR.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c froll.c -o froll.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c frollR.c -o frollR.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c frolladaptive.c -o frolladaptive.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fsort.c -o fsort.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fwrite.c -o fwrite.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c fwriteR.c -o fwriteR.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c gsumm.c -o gsumm.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c ijoin.c -o ijoin.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c init.c -o init.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c inrange.c -o inrange.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c nafill.c -o nafill.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c nqrecreateindices.c -o nqrecreateindices.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c openmp-utils.c -o openmp-utils.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c programming.c -o programming.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c quickselect.c -o quickselect.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c rbindlist.c -o rbindlist.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c reorder.c -o reorder.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c shift.c -o shift.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c snprintf.c -o snprintf.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c subset.c -o subset.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c transpose.c -o transpose.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c types.c -o types.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c uniqlist.c -o uniqlist.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c utils.c -o utils.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c vecseq.c -o vecseq.o
    /opt/local/bin/gcc-mp-7 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/local/include    -fPIC  -pipe -Os -arch ppc  -c wrappers.c -o wrappers.o
    /opt/local/bin/gcc-mp-7 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -arch ppc -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -lz -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    PKG_CFLAGS =
    PKG_LIBS = -lz
    if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
    if [ "" != "Windows_NT" ] && [ uname -s = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
    install_name_tool: object: data_table.so malformed object (unknown load command 7)
    make: *** [all] Error 1
    ERROR: compilation failed for package ‘data.table’
  • removing ‘/Users/svacchanda/Library/R/powerpc/4.1/library/data.table’
  • restoring previous ‘/Users/svacchanda/Library/R/powerpc/4.1/library/data.table’

The downloaded source packages are in
        ‘/private/var/folders/rD/rDeCM6SDHv8daLCecrRmrU+++TI/-Tmp-/RtmpOOJJuH/downloaded_packages’
Warning message:
In install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table") :
  installation of package ‘data.table’ had non-zero exit status`

Session info:

`> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)
Running under: OS X Snow Leopard 10.6

Matrix products: default
BLAS: /opt/local/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /opt/local/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2 `

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