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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:iBMQ.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings iBMQ_1.38.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/iBMQ.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'iBMQ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iBMQ' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... 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 whether package 'iBMQ' can be installed ... WARNING
Found the following significant warnings:
  RngStream.c:321:7: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
See 'F:/biocbuild/bbs-3.16-bioc/meat/iBMQ.Rcheck/00install.out' for details.
* 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 R 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 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 ... OK
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/iBMQ/libs/x64/iBMQ.dll':
  Found '_assert', possibly from 'assert' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
eqtlClassifier 5.71   0.25    5.97
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/iBMQ.Rcheck/00check.log'
for details.

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### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL iBMQ
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'iBMQ' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ARS.c -o ARS.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RngStream.c -o RngStream.o
RngStream.c: In function 'RngStream_CreateStream':
RngStream.c:321:7: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  321 |       strncpy (g->name, name, len + 1);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RngStream.c:319:13: note: length computed here
  319 |       len = strlen (name);
      |             ^~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c iBMQ_common.c -o iBMQ_common.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c main_parallel_sparse_constC.c -o main_parallel_sparse_constC.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c norm_gamma_generation.c -o norm_gamma_generation.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -fopenmp    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sparse.c -o sparse.o
gcc -shared -s -static-libgcc -o iBMQ.dll tmp.def ARS.o RngStream.o iBMQ_common.o main_parallel_sparse.o main_parallel_sparse_constC.o norm_gamma_generation.o sparse.o -L/x64/lib -lgsl -lgslcblas -lm -fopenmp -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-iBMQ/00new/iBMQ/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iBMQ)