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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefilter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefilter_1.89.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/genefilter.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.89.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genefilter’ can be installed ... WARNING
Found the following significant warnings:
  half_range_mode.cpp:100:88: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
  pAUC.c:140:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/genefilter.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
  howtogenefinder.Rmd
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘tkWidgets’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘tkWidgets:::formatArg’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eSetFilter : buildGUI: no visible binding for '<<-' assignment to ‘END’
eSetFilter : buildGUI : setFilter: no visible global function
  definition for ‘tkget’
eSetFilter : buildGUI : setFilter: no visible global function
  definition for ‘tkcurselection’
eSetFilter : buildGUI : setFilter: no visible global function
  definition for ‘writeList’
eSetFilter : buildGUI : setFilter: no visible global function
  definition for ‘tkconfigure’
eSetFilter : buildGUI : cancel: no visible global function definition
  for ‘tkdestroy’
eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment
  to ‘END’
eSetFilter : buildGUI : finish: no visible global function definition
  for ‘tkdestroy’
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for ‘tkget’
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for ‘tkcurselection’
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for ‘tkconfigure’
eSetFilter : buildGUI : viewFilter: no visible global function
  definition for ‘writeText’
eSetFilter : buildGUI : pickedSel: no visible global function
  definition for ‘tkconfigure’
eSetFilter : buildGUI : remove: no visible global function definition
  for ‘tkget’
eSetFilter : buildGUI : remove: no visible global function definition
  for ‘tkcurselection’
eSetFilter : buildGUI : remove: no visible global function definition
  for ‘writeList’
eSetFilter : buildGUI : remove: no visible global function definition
  for ‘tkconfigure’
eSetFilter : buildGUI: no visible global function definition for
  ‘tktoplevel’
eSetFilter : buildGUI: no visible global function definition for
  ‘tktitle<-’
eSetFilter : buildGUI: no visible global function definition for
  ‘tktext’
eSetFilter : buildGUI: no visible global function definition for
  ‘writeText’
eSetFilter : buildGUI: no visible global function definition for
  ‘tkconfigure’
eSetFilter : buildGUI: no visible global function definition for
  ‘tkpack’
eSetFilter : buildGUI: no visible global function definition for
  ‘tkframe’
eSetFilter : buildGUI: no visible global function definition for
  ‘tklabel’
eSetFilter : buildGUI: no visible global function definition for
  ‘makeViewer’
eSetFilter : buildGUI: no visible global function definition for
  ‘tkbind’
eSetFilter : buildGUI: no visible global function definition for
  ‘writeList’
eSetFilter : buildGUI: no visible global function definition for
  ‘tkbutton’
eSetFilter : buildGUI: no visible global function definition for
  ‘tkwait.window’
eSetFilter : buildGUI: no visible binding for global variable ‘END’
getRdAsText: no visible global function definition for ‘.path.package’
isESet: no visible global function definition for ‘tkmessageBox’
setESetArgs: no visible global function definition for ‘tkdestroy’
setESetArgs : cancel: no visible global function definition for
  ‘tkdestroy’
setESetArgs : end: no visible global function definition for
  ‘tkdestroy’
setESetArgs: no visible global function definition for ‘tktoplevel’
setESetArgs: no visible global function definition for ‘tktitle<-’
setESetArgs: no visible global function definition for ‘tkgrid’
setESetArgs: no visible global function definition for ‘tklabel’
setESetArgs: no visible global function definition for ‘tclVar’
setESetArgs: no visible global function definition for ‘tkframe’
setESetArgs: no visible global function definition for ‘makeViewer’
setESetArgs: no visible global function definition for ‘writeText’
setESetArgs: no visible global function definition for ‘tkconfigure’
setESetArgs: no visible global function definition for ‘tkentry’
setESetArgs: no visible global function definition for ‘tkbind’
setESetArgs: no visible global function definition for
  ‘tkgrid.configure’
setESetArgs: no visible global function definition for ‘tkbutton’
setESetArgs: no visible global function definition for ‘tkpack’
setESetArgs: no visible global function definition for ‘tkwait.window’
setESetArgs: no visible global function definition for ‘tclvalue’
showESet : end: no visible global function definition for ‘tkdestroy’
showESet: no visible global function definition for ‘tktoplevel’
showESet: no visible global function definition for ‘tktitle<-’
showESet: no visible global function definition for ‘tkframe’
showESet: no visible global function definition for ‘makeViewer’
showESet: no visible global function definition for ‘writeList’
showESet: no visible global function definition for ‘tkpack’
showESet: no visible global function definition for ‘tkbutton’
Undefined global functions or variables:
  .path.package END makeViewer tclVar tclvalue tkbind tkbutton
  tkconfigure tkcurselection tkdestroy tkentry tkframe tkget tkgrid
  tkgrid.configure tklabel tkmessageBox tkpack tktext tktitle<-
  tktoplevel tkwait.window writeList writeText
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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/4.5-arm64/Resources/library/genefilter/libs/genefilter.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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 usage of KIND in Fortran files ... OK
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/genefilter.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genefilter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘genefilter’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c half_range_mode.cpp -o half_range_mode.o
half_range_mode.cpp:100:88: warning: format specifies type 'int' but the argument has type 'size_type' (aka 'unsigned long') [-Wformat]
    if (diag) Rprintf( "N = %i, N'' = %i, w = %.4f, |J| = %i\n", N, N_double_prime, w, J.size() );
                                                          ~~                           ^~~~~~~~
                                                          %zu
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.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 nd.c -o nd.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 pAUC.c -o pAUC.o
pAUC.c:140:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
    if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pAUC.c:140:8: note: cast one or both operands to int to silence this warning
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rowPAUCs.c -o rowPAUCs.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 rowttests.c -o rowttests.o
/opt/gfortran/bin/gfortran -arch arm64  -fPIC  -Wall -g -O2  -c ttest.f -o ttest.o
ttest.f:47:12:

   47 |          dm=dm1-dm2
      |            1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:50:12:

   50 |          dm=dm1/dm2
      |            1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:59:13:

   59 |          tst=(dm1-dm2)/sqrt((1.d0/ng1+1.d0/ng2)*(dss1+dss2)/(ng1+ng2-2))
      |             1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:62:10:

   62 |       tst=(dm1-dm2)/sqrt(dss1/((ng1-1)*ng1)+dss2/((ng2-1)*ng2))
      |          1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.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
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-genefilter/00new/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (genefilter)