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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IRISFGM_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/IRISFGM.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRISFGM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IRISFGM’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘IRISFGM’ can be installed ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 is not available
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/IRISFGM.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IRISFGM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘IRISFGM’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c cluster.cpp -o cluster.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c expand.cpp -o expand.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c get_options.cpp -o get_options.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getline.c -o getline.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c main.cpp -o main.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c make_graph.cpp -o make_graph.o
make_graph.cpp:51:5: warning: variable 'i' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
    i++;
    ^
make_graph.cpp:45:29: note: incremented here
  for (int i = 0; i < cols; i++) {
                            ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c read_array.cpp -o read_array.o
read_array.cpp:882:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
        fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
                        ~~                ^~~~~~~~~~~~~
                        %lu
read_array.cpp:1376:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
        fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
                        ~~                ^~~~~~~~~~~~~
                        %lu
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c struct.cpp -o struct.o
struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable]
  static long lastTime = 0;
              ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -DVER=2.08 -fPIC  -Wall -g -O2  -c write_block.cpp -o write_block.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o IRISFGM.so RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-IRISFGM/00new/IRISFGM/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘ReadFrom10X_h5’ in package ‘IRISFGM’
Creating a generic function from function ‘ReadFrom10X_folder’ in package ‘IRISFGM’
** 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 (IRISFGM)