##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GLAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GLAD_2.72.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GLAD.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.72.0’
* 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 ‘GLAD’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 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 ... WARNING
Missing or unexported object: ‘aws::laws’
* 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 ... WARNING
checkRd: (5) as.profileCGH.Rd:25: \item in \value must have non-empty label
checkRd: (-1) daglad.Rd:47: Escaped LaTeX specials: \$
checkRd: (5) daglad.Rd:182-183: \item in \value must have non-empty label
checkRd: (-1) daglad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:196-199: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:202-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:207-210: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:213-216: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:218: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:221-224: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:226-228: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:240: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:241: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:242-243: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:244: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:245: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:246: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:247-248: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) daglad.Rd:249: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (5) glad.Rd:152: \item in \value must have non-empty label
checkRd: (-1) glad.Rd:159-160: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:162-165: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:168-171: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:173-176: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:178-179: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:182-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:189-190: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:192-193: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:195-196: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:213: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:214: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) glad.Rd:224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glad.Rd:225: Lost braces in \itemize; meant \describe ?
checkRd: (-1) glad.Rd:226: Lost braces in \itemize; meant \describe ?
* 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/GLAD/libs/GLAD.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (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 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GLAD.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GLAD
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘GLAD’ ...
** this is package ‘GLAD’ version ‘2.72.0’
** using staged installation
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -L/opt/R/arm64/lib -lgsl -lgslcblas -lm
PKG_CPPFLAGS = -DIS_MAC_OS

** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c BkpInfo.cpp -o BkpInfo.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c HaarSeg.cpp -o HaarSeg.o
HaarSeg.cpp:50:12: warning: variable 'lowSquareSum' set but not used [-Wunused-but-set-variable]
    double lowSquareSum = 0;
           ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MoveBkp.cpp -o MoveBkp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c OutliersGNL.cpp -o OutliersGNL.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c chrBreakpoints.cpp -o chrBreakpoints.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cutree.cpp -o cutree.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c daglad.cpp -o daglad.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c distance.cpp -o distance.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c filterBkp.cpp -o filterBkp.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c findCluster.cpp -o findCluster.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c glad-utils.cpp -o glad-utils.o
glad-utils.cpp:862:27: warning: unused variable 'it_new_end_NormalCluster' [-Wunused-variable]
    vector<int>::iterator it_new_end_NormalCluster;
                          ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c hclust.cpp -o hclust.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c laws.c -o laws.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c loopRemove.cpp -o loopRemove.o
loopRemove.cpp:38:9: warning: variable 'nb_loop' set but not used [-Wunused-but-set-variable]
    int nb_loop = 0;
        ^
1 warning generated.
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 GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/opt/R/arm64/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-GLAD/00new/GLAD/libs
** R
** data
** demo
** 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 (GLAD)