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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneSelectMMD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneSelectMMD_2.44.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneSelectMMD.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneSelectMMD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneSelectMMD’ version ‘2.44.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GeneSelectMMD’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/GeneSelectMMD/libs/GeneSelectMMD.so’:
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneSelectMMD.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneSelectMMD
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GeneSelectMMD’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GeneSelectMMD_init.c -o GeneSelectMMD_init.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c Qfunc.f -o Qfunc.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c blas.f -o blas.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c isnan.c -o isnan.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c lbfgsb.f -o lbfgsb.o
lbfgsb.f:1409:25:

 1409 |      +                 tu,tl,wmc,wmp,wmw,ddot,tj,tj0,neggi,sbgnrm,
      |                         ^
Warning: ‘tu’ may be used uninitialized [-Wmaybe-uninitialized]
lbfgsb.f:1482:72:

 1482 |                t(nbreak) = tl/(-neggi)
      |                                                                        ^
Warning: ‘tl’ may be used uninitialized [-Wmaybe-uninitialized]
lbfgsb.f:1409:28:

 1409 |      +                 tu,tl,wmc,wmp,wmw,ddot,tj,tj0,neggi,sbgnrm,
      |                            ^
note: ‘tl’ was declared here
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c lbfgsbDriver.f -o lbfgsbDriver.o
lbfgsbDriver.f:243:71:

  243 |      +                 wa(2*mmax*nmax + 5*nmax + 11*mmax*mmax + 8*mmax)
      |                                                                       1
Warning: Array ‘wa’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c linpack.f -o linpack.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c llkhFun.f -o llkhFun.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c myTtest.f -o myTtest.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c paraEstLoop.f -o paraEstLoop.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pt.c -o pt.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c timer.f -o timer.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c wiFun.f -o wiFun.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GeneSelectMMD.so GeneSelectMMD_init.o Qfunc.o blas.o isnan.o lbfgsb.o lbfgsbDriver.o linpack.o llkhFun.o myTtest.o paraEstLoop.o pt.o timer.o wiFun.o -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for _negqfunc_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _dnegqfunc_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _dcopy_: register 22 saved somewhere other than in frame
ld: warning: could not create compact unwind for _prn1lb_.part.0: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _prn3lb_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _matupd_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _prn2lb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _dcsrch_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _lnsrlb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _subsm_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _freev_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _cauchy_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _active_: registers 19 and 20 not saved contiguously in frame
ld: warning: could not create compact unwind for _mainlb_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _setulb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _lbfgsbdriver_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _dtrsl_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _llkhfun_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for _myttest_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _paraestloop_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _wifun_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-GeneSelectMMD/00new/GeneSelectMMD/libs
** R
** 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 (GeneSelectMMD)