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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 803/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneticsPed 1.69.0  (landing page)
David Henderson
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/GeneticsPed
git_branch: devel
git_last_commit: 48e7cab
git_last_commit_date: 2024-10-29 09:27:45 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


BUILD results for GeneticsPed on kunpeng2

To the developers/maintainers of the GeneticsPed package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneticsPed.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GeneticsPed
Version: 1.69.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeneticsPed
StartedAt: 2024-12-23 23:10:15 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:10:32 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 17.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GeneticsPed
###
##############################################################################
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* checking for file ‘GeneticsPed/DESCRIPTION’ ... OK
* preparing ‘GeneticsPed’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘GeneticsPed’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c ainverse.cc -o ainverse.o
In file included from ../include/ainverse.h:20,
                 from ainverse.cc:9:
../include/pedtemplate.h:18:9: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c eibd.cc -o eibd.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran  -fPIC  -g -O2  -Wall -Werror=format-security -c ggmatmult.f -o ggmatmult.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran  -fPIC  -g -O2  -Wall -Werror=format-security -c gpi.f -o gpi.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c inbreed.cc -o inbreed.o
In file included from ../include/inbreed.h:18,
                 from inbreed.cc:10:
../include/pedtemplate.h:18:9: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c inverseAdditive.cc -o inverseAdditive.o
inverseAdditive.cc:1:9: warning: "R_NO_REMAP" redefined
    1 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c meuwissen.cc -o meuwissen.o
meuwissen.cc:1:9: warning: "R_NO_REMAP" redefined
    1 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c pedSort.cc -o pedSort.o
pedSort.cc:1:9: warning: "R_NO_REMAP" redefined
    1 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c pedtemplate.cc -o pedtemplate.o
In file included from pedtemplate.cc:15:
../include/pedtemplate.h:18:9: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
pedtemplate.cc: In member function ‘void Pedigree::ShowPed()’:
pedtemplate.cc:373:15: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘__gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type’ {aka ‘long int’} [-Wformat=]
  373 |     Rprintf("%d\t", p - pedigree.begin());
      |              ~^     ~~~~~~~~~~~~~~~~~~~~
      |               |       |
      |               int     __gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type {aka long int}
      |              %ld
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c register.cc -o register.o
In file included from ../include/../include/inbreed.h:18,
                 from ../include/meuwissen.h:7,
                 from register.cc:8:
../include/../include/pedtemplate.h:18:9: warning: "R_NO_REMAP" redefined
   18 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function ‘sargolzaei’:
sargolzaei.c:52:32: warning: ‘*Ped[S][0]’ may be used uninitialized [-Wmaybe-uninitialized]
   52 |       rPed[rN][0] = Link[Ped[S][0]];
      |                          ~~~~~~^~~
sargolzaei.c:53:34: warning: ‘*Ped[D][1]’ may be used uninitialized [-Wmaybe-uninitialized]
   53 |       rPed[rN++][1] = Link[Ped[D][1]];
      |                            ~~~~~~^~~
sargolzaei.c:58:32: warning: ‘*Ped[D][0]’ may be used uninitialized [-Wmaybe-uninitialized]
   58 |       rPed[rN][0] = Link[Ped[D][0]];
      |                          ~~~~~~^~~
sargolzaei.c:59:34: warning: ‘*Ped[D][1]’ may be used uninitialized [-Wmaybe-uninitialized]
   59 |       rPed[rN++][1] = Link[Ped[D][1]];
      |                            ~~~~~~^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c sortped.cc -o sortped.o
In file included from sortped.cc:1:
../include/sortped.h:5:9: warning: "R_NO_REMAP" redefined
    5 | #define R_NO_REMAP
      |         ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
sortped.cc: In function ‘void SortPed(Pedigree&, TPedVec&)’:
sortped.cc:55:5: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
   55 |     error("Problems in pedigree.  Stopping inbreeding calculations\n");
      |     ^~~~~
      |     perror
make: *** [/home/biocbuild/R/R/etc/Makeconf:202: sortped.o] Error 1
ERROR: compilation failed for package ‘GeneticsPed’
* removing ‘/home/biocbuild/tmp/RtmpxMM72M/Rinst2faf0e4b29257c/GeneticsPed’
      -----------------------------------
ERROR: package installation failed