McCall N. Matthew
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/ternarynet |
| git_branch: devel |
| git_last_commit: 251d20a |
| git_last_commit_date: 2024-10-29 09:40:14 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:47 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 2117/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ternarynet 1.51.0 (landing page) McCall N. Matthew
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the ternarynet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ternarynet.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. |
| Package: ternarynet |
| Version: 1.51.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ternarynet |
| StartedAt: 2025-01-04 02:48:55 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 02:48:58 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 3.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ternarynet
###
##############################################################################
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* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* preparing ‘ternarynet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (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-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c array.c -o array.o
/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 gn.c -o gn.o
gn.c: In function ‘score’:
gn.c:486: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
486 | #pragma omp parallel for
gn.c:493: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
493 | #pragma omp atomic
/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 gn_Rwrap.c -o gn_Rwrap.o
/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 init.c -o init.o
/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 tnetfit.cc -o tnetfit.o
tnetfit.cc: In function ‘SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
tnetfit.cc:35:32: error: ‘coerceVector’ was not declared in this scope; did you mean ‘Rf_coerceVector’?
35 | perturbationType = INTEGER(coerceVector(RperturbationType, INTSXP))[0];
| ^~~~~~~~~~~~
| Rf_coerceVector
In file included from /home/biocbuild/R/R/include/Rdefines.h:41,
from tnetfit.cc:12:
tnetfit.cc:220:23: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
220 | PROTECT(Routput = allocVector(VECSXP, 14));
| ^~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
388 | #define PROTECT(s) Rf_protect(s)
| ^
tnetfit.cc:311:33: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’?
311 | SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
| ^~~~~~~~~~
| Rf_ScalarReal
tnetfit.cc:315:33: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
315 | SET_VECTOR_ELT(Routput, 12, ScalarInteger(stage_count));
| ^~~~~~~~~~~~~
| Rf_ScalarInteger
tnetfit.cc:320:29: error: ‘mkChar’ was not declared in this scope
320 | SET_STRING_ELT(Rnames,0,mkChar("degreeObj"));
| ^~~~~~
tnetfit.cc:334:5: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’?
334 | setAttrib(Routput, R_NamesSymbol, Rnames);
| ^~~~~~~~~
| Rf_setAttrib
tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable]
73 | int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
| ^~~~~
make: *** [/home/biocbuild/R/R/etc/Makeconf:202: tnetfit.o] Error 1
ERROR: compilation failed for package ‘ternarynet’
* removing ‘/home/biocbuild/tmp/RtmpQtabac/Rinst156c4d24c2bd7f/ternarynet’
-----------------------------------
ERROR: package installation failed