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This page was generated on 2022-04-13 12:05:29 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

INSTALL results for iBMQ on nebbiolo2


To the developers/maintainers of the iBMQ package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 901/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iBMQ 1.34.0  (landing page)
Greg Imholte
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/iBMQ
git_branch: RELEASE_3_14
git_last_commit: 77b19ee
git_last_commit_date: 2021-10-26 12:05:59 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: iBMQ
Version: 1.34.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL iBMQ
StartedAt: 2022-04-12 03:16:29 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 03:16:38 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 8.3 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL iBMQ
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘iBMQ’ ...
** using staged installation
checking for gcc... 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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... 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
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c ARS.c -o ARS.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c RngStream.c -o RngStream.o
In file included from /usr/include/string.h:495,
                 from RngStream.c:17:
In function ‘strncpy’,
    inlined from ‘RngStream_CreateStream’ at RngStream.c:321:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RngStream.c: In function ‘RngStream_CreateStream’:
RngStream.c:319:13: note: length computed here
  319 |       len = strlen (name);
      |             ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c iBMQ_common.c -o iBMQ_common.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c main_parallel_sparse.c -o main_parallel_sparse.o
main_parallel_sparse.c: In function ‘iBMQ_main’:
main_parallel_sparse.c:255:5: warning: ‘Cfile’ may be used uninitialized in this function [-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:255:5: warning: ‘Sig2file’ may be used uninitialized in this function [-Wmaybe-uninitialized]
main_parallel_sparse.c:255:5: warning: ‘Mufile’ may be used uninitialized in this function [-Wmaybe-uninitialized]
main_parallel_sparse.c:255:5: warning: ‘Bfile’ may be used uninitialized in this function [-Wmaybe-uninitialized]
main_parallel_sparse.c:255:5: warning: ‘Afile’ may be used uninitialized in this function [-Wmaybe-uninitialized]
main_parallel_sparse.c:255:5: warning: ‘Pfile’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c norm_gamma_generation.c -o norm_gamma_generation.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c sparse.c -o sparse.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/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/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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)