Greg Imholte
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/iBMQ |
| git_branch: devel |
| git_last_commit: f5a261f |
| git_last_commit_date: 2024-10-29 09:43:53 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| 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" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R 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 988/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iBMQ 1.47.0 (landing page) Greg Imholte
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the iBMQ package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iBMQ.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: iBMQ |
| Version: 1.47.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL iBMQ |
| StartedAt: 2024-12-23 19:32:51 -0000 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 19:33:06 -0000 (Mon, 23 Dec 2024) |
| EllapsedTime: 15.3 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL iBMQ
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘iBMQ’ ...
** using staged installation
checking for gcc... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc accepts -g... yes
checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking omp.h usability... yes
checking omp.h presence... yes
checking for omp.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (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 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c ARS.c -o ARS.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 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RngStream.c -o RngStream.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 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c iBMQ_common.c -o iBMQ_common.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 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c main_parallel_sparse.c -o main_parallel_sparse.o
main_parallel_sparse.c: In function ‘iBMQ_main’:
main_parallel_sparse.c:255:33: warning: ‘Pfile’ may be used uninitialized [-Wmaybe-uninitialized]
255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
256 | n_snps, n_genes, A, B, P, Mu, Sig2, C);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main_parallel_sparse.c:83:15: note: ‘Pfile’ was declared here
83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile;
| ^~~~~
main_parallel_sparse.c:255:33: warning: ‘Afile’ may be used uninitialized [-Wmaybe-uninitialized]
255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
256 | n_snps, n_genes, A, B, P, Mu, Sig2, C);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main_parallel_sparse.c:83:23: note: ‘Afile’ was declared here
83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile;
| ^~~~~
main_parallel_sparse.c:255:33: warning: ‘Bfile’ may be used uninitialized [-Wmaybe-uninitialized]
255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
256 | n_snps, n_genes, A, B, P, Mu, Sig2, C);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main_parallel_sparse.c:83:31: note: ‘Bfile’ was declared here
83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile;
| ^~~~~
main_parallel_sparse.c:255:33: warning: ‘Mufile’ may be used uninitialized [-Wmaybe-uninitialized]
255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
256 | n_snps, n_genes, A, B, P, Mu, Sig2, C);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main_parallel_sparse.c:83:39: note: ‘Mufile’ was declared here
83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile;
| ^~~~~~
main_parallel_sparse.c:255:33: warning: ‘Sig2file’ may be used uninitialized [-Wmaybe-uninitialized]
255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
256 | n_snps, n_genes, A, B, P, Mu, Sig2, C);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main_parallel_sparse.c:83:48: note: ‘Sig2file’ was declared here
83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile;
| ^~~~~~~~
main_parallel_sparse.c:255:33: warning: ‘Cfile’ may be used uninitialized [-Wmaybe-uninitialized]
255 | store_mcmc_output(Afile, Bfile, Pfile, Mufile, Sig2file, Cfile,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
256 | n_snps, n_genes, A, B, P, Mu, Sig2, C);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main_parallel_sparse.c:83:59: note: ‘Cfile’ was declared here
83 | FILE *Pfile, *Afile, *Bfile, *Mufile, *Sig2file, *Cfile;
| ^~~~~
/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 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.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 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c norm_gamma_generation.c -o norm_gamma_generation.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 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c sparse.c -o sparse.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o iBMQ.so ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -lgsl -lgslcblas -lm -lgomp -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-iBMQ/00new/iBMQ/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (iBMQ)