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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:iBMQ.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings iBMQ_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/iBMQ.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘iBMQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iBMQ’ version ‘1.46.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘iBMQ’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eqtlMcmc: no visible global function definition for ‘is’
eqtlMcmc: no visible global function definition for ‘exprs’
Undefined global functions or variables:
  exprs is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/iBMQ/libs/iBMQ.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/iBMQ.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL iBMQ
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c ARS.c -o ARS.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c RngStream.c -o RngStream.o
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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:255:33: 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;
      |                                                           ^~~~~
gcc -I"/home/biocbuild/bbs-3.20-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-3.20-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-3.20-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-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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)