CRAN Package Check Results for Package brt

Last updated on 2019-09-17 22:48:03 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3.0 3.40 141.70 145.10 OK
r-devel-linux-x86_64-debian-gcc 1.3.0 2.88 104.19 107.07 OK
r-devel-linux-x86_64-fedora-clang 1.3.0 185.64 OK
r-devel-linux-x86_64-fedora-gcc 1.3.0 163.59 OK
r-devel-windows-ix86+x86_64 1.3.0 22.00 163.00 185.00 OK
r-patched-linux-x86_64 1.3.0 3.29 131.28 134.57 OK
r-patched-solaris-x86 1.3.0 262.60 OK
r-release-linux-x86_64 1.3.0 3.30 142.82 146.12 OK
r-release-windows-ix86+x86_64 1.3.0 11.00 158.00 169.00 OK
r-release-osx-x86_64 1.3.0 FAIL
r-oldrel-windows-ix86+x86_64 1.3.0 9.00 161.00 170.00 OK
r-oldrel-osx-x86_64 1.3.0 NOTE

Check Details

Version: 1.3.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'vsn', 'DESeq2', 'pasilla'
Flavor: r-release-osx-x86_64

Version: 1.3.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘brt.rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocInstaller_1.30.0.tar.gz'
    Content type 'application/x-gzip' length 19149 bytes (18 KB)
    ==================================================
    downloaded 18 KB
    
    * installing *source* package ‘BiocInstaller’ ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
    A newer version of Bioconductor is available for this version of R,
     ?BiocUpgrade for help
    ** testing if installed package can be loaded from final location
    Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
    A newer version of Bioconductor is available for this version of R,
     ?BiocUpgrade for help
    ** testing if installed package keeps a record of temporary installation path
    * DONE (BiocInstaller)
    
    The downloaded source packages are in
     '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmppy9lkq/downloaded_packages'
    trying URL 'https://bioconductor.org/packages/3.7/data/experiment/src/contrib/pasilla_1.8.0.tar.gz'
    Content type 'application/x-gzip' length 3868640 bytes (3.7 MB)
    ==================================================
    downloaded 3.7 MB
    
    * installing *source* package ‘pasilla’ ...
    ** using staged installation
    ** data
    ** inst
    ** 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 (pasilla)
    
    The downloaded source packages are in
     '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmppy9lkq/downloaded_packages'
    trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz'
    Content type 'application/x-gzip' length 8204728 bytes (7.8 MB)
    ==================================================
    downloaded 7.8 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/zlibbioc_1.26.0.tar.gz'
    Content type 'application/x-gzip' length 257340 bytes (251 KB)
    ==================================================
    downloaded 251 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/GenomeInfoDb_1.16.0.tar.gz'
    Content type 'application/x-gzip' length 3402260 bytes (3.2 MB)
    ==================================================
    downloaded 3.2 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/XVector_0.20.0.tar.gz'
    Content type 'application/x-gzip' length 64240 bytes (62 KB)
    ==================================================
    downloaded 62 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/DelayedArray_0.6.6.tar.gz'
    Content type 'application/x-gzip' length 486899 bytes (475 KB)
    ==================================================
    downloaded 475 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/AnnotationDbi_1.42.1.tar.gz'
    Content type 'application/x-gzip' length 4337155 bytes (4.1 MB)
    ==================================================
    downloaded 4.1 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/annotate_1.58.0.tar.gz'
    Content type 'application/x-gzip' length 1867576 bytes (1.8 MB)
    ==================================================
    downloaded 1.8 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/S4Vectors_0.18.3.tar.gz'
    Content type 'application/x-gzip' length 627235 bytes (612 KB)
    ==================================================
    downloaded 612 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/IRanges_2.14.12.tar.gz'
    Content type 'application/x-gzip' length 458366 bytes (447 KB)
    ==================================================
    downloaded 447 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/GenomicRanges_1.32.7.tar.gz'
    Content type 'application/x-gzip' length 1116540 bytes (1.1 MB)
    ==================================================
    downloaded 1.1 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/SummarizedExperiment_1.10.1.tar.gz'
    Content type 'application/x-gzip' length 1178107 bytes (1.1 MB)
    ==================================================
    downloaded 1.1 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocGenerics_0.26.0.tar.gz'
    Content type 'application/x-gzip' length 45638 bytes (44 KB)
    ==================================================
    downloaded 44 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/Biobase_2.40.0.tar.gz'
    Content type 'application/x-gzip' length 1657220 bytes (1.6 MB)
    ==================================================
    downloaded 1.6 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocParallel_1.14.2.tar.gz'
    Content type 'application/x-gzip' length 884432 bytes (863 KB)
    ==================================================
    downloaded 863 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/genefilter_1.62.0.tar.gz'
    Content type 'application/x-gzip' length 1432307 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/geneplotter_1.58.0.tar.gz'
    Content type 'application/x-gzip' length 1428691 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/DESeq2_1.20.0.tar.gz'
    Content type 'application/x-gzip' length 2059356 bytes (2.0 MB)
    ==================================================
    downloaded 2.0 MB
    
    * installing *source* package ‘GenomeInfoDbData’ ...
    ** using staged installation
    ** data
    ** inst
    ** help
    *** installing help indices
    ** building package indices
    ** 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 (GenomeInfoDbData)
    * installing *source* package ‘zlibbioc’ ...
    ** using staged installation
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    mkdir -p "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-zlibbioc/00new/zlibbioc/include"
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_zlibbioc.c -o R_init_zlibbioc.o
    clang -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 zlibbioc.so R_init_zlibbioc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-zlibbioc/00new/zlibbioc/libs
    generating debug symbols (dSYM)
    warning: no debug symbols in executable (-arch x86_64)
    ** R
    ** 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 (zlibbioc)
    * installing *source* package ‘BiocGenerics’ ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Creating a new generic function for ‘append’ in package ‘BiocGenerics’
    Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
    Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
    Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
    Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
    Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
    Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
    Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
    Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
    Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
    Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
    Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
    Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
    Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
    Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
    Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
    Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
    Creating a new generic function for ‘get’ in package ‘BiocGenerics’
    Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
    Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
    Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
    Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
    Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘match’ in package ‘BiocGenerics’
    Creating a new generic function for ‘order’ in package ‘BiocGenerics’
    Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
    Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
    Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
    Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
    Creating a new generic function for ‘union’ in package ‘BiocGenerics’
    Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
    Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
    Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
    Creating a new generic function for ‘table’ in package ‘BiocGenerics’
    Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
    Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
    Creating a new generic function for ‘var’ in package ‘BiocGenerics’
    Creating a new generic function for ‘sd’ in package ‘BiocGenerics’
    Creating a new generic function for ‘which’ in package ‘BiocGenerics’
    Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
    Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
    Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
    Creating a new generic function for ‘mad’ in package ‘BiocGenerics’
    Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
    Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’
    Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’
    Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’
    Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’
    Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
    Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
    Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
    Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’
    Creating a new generic function for ‘basename’ in package ‘BiocGenerics’
    Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’
    ** help
    *** installing help indices
    ** building package indices
    ** 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 (BiocGenerics)
    * installing *source* package ‘BiocParallel’ ...
    ** using staged installation
    ** libs
    clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ipcmutex.cpp -o ipcmutex.o
    In file included from ipcmutex.cpp:1:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/uuid/uuid_generators.hpp:17:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/uuid/random_generator.hpp:17:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/mersenne_twister.hpp:30:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/seed_impl.hpp:26:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/const_mod.hpp:23:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/large_arithmetic.hpp:19:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/integer_log2.hpp:19:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
    BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
    ^
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
    # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
     ^
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
    # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
     ^
    <scratch space>:40:2: note: expanded from here
     message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
     ^
    1 warning generated.
    clang++ -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 BiocParallel.so ipcmutex.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-BiocParallel/00new/BiocParallel/libs
    generating debug symbols (dSYM)
    ** R
    ** 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 (BiocParallel)
    * installing *source* package ‘S4Vectors’ ...
    ** using staged installation
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c AEbufs.c -o AEbufs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c DataFrame_class.c -o DataFrame_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Hits_class.c -o Hits_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c LLint_class.c -o LLint_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c List_class.c -o List_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rle_class.c -o Rle_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rle_utils.c -o Rle_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c SEXP_utils.c -o SEXP_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c SimpleList_class.c -o SimpleList_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c anyMissing.c -o anyMissing.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c character_utils.c -o character_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c eval_utils.c -o eval_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c hash_utils.c -o hash_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c integer_utils.c -o integer_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c logical_utils.c -o logical_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c safe_arithm.c -o safe_arithm.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sort_utils.c -o sort_utils.o
    sort_utils.c:263:13: warning: unused function 'sort_uchar_array' [-Wunused-function]
    static void sort_uchar_array(unsigned char *x, int nelt, int desc)
     ^
    1 warning generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c subsetting_utils.c -o subsetting_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c vector_utils.c -o vector_utils.o
    clang -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 S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-S4Vectors/00new/S4Vectors/libs
    generating debug symbols (dSYM)
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
    Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
    Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
    Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
    Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
    Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
    Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
    Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
    Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
    Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
    in method for ‘coerce’ with signature ‘"data.table","DataFrame"’: no definition for class “data.table”
    ** 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 (S4Vectors)
    * installing *source* package ‘Biobase’ ...
    ** using staged installation
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rinit.c -o Rinit.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c anyMissing.c -o anyMissing.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c envir.c -o envir.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c matchpt.c -o matchpt.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rowMedians.c -o rowMedians.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sublist_extract.c -o sublist_extract.o
    clang -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 Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-Biobase/00new/Biobase/libs
    generating debug symbols (dSYM)
    ** 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
    ** 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 (Biobase)
    * installing *source* package ‘IRanges’ ...
    ** using staged installation
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c CompressedList_class.c -o CompressedList_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Grouping_class.c -o Grouping_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IPosRanges_comparison.c -o IPosRanges_comparison.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_class.c -o IRanges_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_constructor.c -o IRanges_constructor.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c NCList.c -o NCList.o
    NCList.c:202:22: warning: unused function 'next_top_down' [-Wunused-function]
    static const NCList *next_top_down(const NCList *nclist)
     ^
    NCList.c:1173:13: warning: function 'NCList_get_y_overlaps_rec' is not needed and will not be emitted [-Wunneeded-internal-declaration]
    static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
     ^
    2 warnings generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_IRanges.c -o R_init_IRanges.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Ranges_class.c -o Ranges_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RleViews_utils.c -o RleViews_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c coverage_methods.c -o coverage_methods.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c extractListFragments.c -o extractListFragments.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I/usr/local/include -fPIC -Wall -g -O2 -c inter_range_methods.c -o inter_range_methods.o
    clang -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 IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-IRanges/00new/IRanges/libs
    generating debug symbols (dSYM)
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
    Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
    Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
    Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
    Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
    Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
    Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
    Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
    ** 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 (IRanges)
    * installing *source* package ‘GenomeInfoDb’ ...
    ** using staged installation
    ** R
    ** 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 (GenomeInfoDb)
    * installing *source* package ‘XVector’ ...
    ** using staged installation
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RDS_random_access.c -o RDS_random_access.o
    RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
     SEXP subscript, ans;
     ^
    1 warning generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_XVector.c -o R_init_XVector.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c SharedDouble_class.c -o SharedDouble_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c SharedInteger_class.c -o SharedInteger_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c SharedRaw_class.c -o SharedRaw_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c SharedVector_class.c -o SharedVector_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c XRawList_comparison.c -o XRawList_comparison.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c XVectorList_class.c -o XVectorList_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c XVector_class.c -o XVector_class.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c io_utils.c -o io_utils.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c slice_methods.c -o slice_methods.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c vector_copy.c -o vector_copy.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c view_summarization_methods.c -o view_summarization_methods.o
    clang -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 XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-XVector/00new/XVector/libs
    generating debug symbols (dSYM)
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** 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 (XVector)
    * installing *source* package ‘DelayedArray’ ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Creating a new generic function for ‘aperm’ in package ‘DelayedArray’
    in method for ‘coerce’ with signature ‘"DelayedMatrix","dgCMatrix"’: no definition for class “dgCMatrix”
    in method for ‘coerce’ with signature ‘"DelayedMatrix","sparseMatrix"’: no definition for class “sparseMatrix”
    Creating a generic function for ‘sweep’ from package ‘base’ in package ‘DelayedArray’
    Creating a new generic function for ‘apply’ in package ‘DelayedArray’
    Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
    Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
    Creating a new generic function for ‘rowMaxs’ in package ‘DelayedArray’
    Creating a new generic function for ‘colMaxs’ in package ‘DelayedArray’
    Creating a new generic function for ‘rowMins’ in package ‘DelayedArray’
    Creating a new generic function for ‘colMins’ in package ‘DelayedArray’
    Creating a new generic function for ‘rowRanges’ in package ‘DelayedArray’
    Creating a new generic function for ‘colRanges’ in package ‘DelayedArray’
    ** 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 (DelayedArray)
    * installing *source* package ‘AnnotationDbi’ ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
    Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
    Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
    Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
    Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
    ** 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 (AnnotationDbi)
    * installing *source* package ‘annotate’ ...
    ** using staged installation
    ** 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 (annotate)
    * installing *source* package ‘GenomicRanges’ ...
    ** using staged installation
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/S4Vectors/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/IRanges/include" -I/usr/local/include -fPIC -Wall -g -O2 -c transcript_utils.c -o transcript_utils.o
    clang -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 GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-GenomicRanges/00new/GenomicRanges/libs
    generating debug symbols (dSYM)
    ** R
    ** 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 (GenomicRanges)
    * installing *source* package ‘SummarizedExperiment’ ...
    ** using staged installation
    ** R
    ** 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 (SummarizedExperiment)
    * installing *source* package ‘genefilter’ ...
    ** using staged installation
    ** libs
    clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c half_range_mode.cpp -o half_range_mode.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nd.c -o nd.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pAUC.c -o pAUC.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rowPAUCs.c -o rowPAUCs.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rowttests.c -o rowttests.o
    gfortran -fPIC -Wall -g -O2 -c ttest.f -o ttest.o
    ttest.f:47:12:
    
     dm=dm1-dm2
     1
    Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
    ttest.f:50:12:
    
     dm=dm1/dm2
     1
    Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
    ttest.f:59:13:
    
     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:
    
     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++ -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 genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-genefilter/00new/genefilter/libs
    generating debug symbols (dSYM)
    ** 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)
    * installing *source* package ‘geneplotter’ ...
    ** using staged installation
    ** 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 (geneplotter)
    * installing *source* package ‘DESeq2’ ...
    ** using staged installation
    ** libs
    clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/Rcpp/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c DESeq2.cpp -o DESeq2.o
    clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/Rcpp/include" -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
    clang++ -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 DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-DESeq2/00new/DESeq2/libs
    generating debug symbols (dSYM)
    ** R
    ** 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 (DESeq2)
    
    The downloaded source packages are in
     '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmppy9lkq/downloaded_packages'
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/affyio_1.50.0.tar.gz'
    Content type 'application/x-gzip' length 109433 bytes (106 KB)
    ==================================================
    downloaded 106 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/preprocessCore_1.42.0.tar.gz'
    Content type 'application/x-gzip' length 122828 bytes (119 KB)
    ==================================================
    downloaded 119 KB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/affy_1.58.0.tar.gz'
    Content type 'application/x-gzip' length 1316488 bytes (1.3 MB)
    ==================================================
    downloaded 1.3 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/limma_3.36.5.tar.gz'
    Content type 'application/x-gzip' length 1466622 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/vsn_3.48.1.tar.gz'
    Content type 'application/x-gzip' length 1842939 bytes (1.8 MB)
    ==================================================
    downloaded 1.8 MB
    
    * installing *source* package ‘affyio’ ...
    ** using staged installation
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -E
    checking for grep that handles long lines and -e... /usr/bin/grep
    checking for egrep... /usr/bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking for main in -lz... yes
    checking zlib.h usability... yes
    checking zlib.h presence... yes
    checking for zlib.h... yes
    checking if zlib version >= 1.1.3... yes
    checking for pthread_create in -lpthread... yes
    checking if we can use pthreads... yes
    checking if PTHREAD_STACK_MIN is defined... yes
    configure: Enabling threading for affyio
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c fread_functions.c -o fread_functions.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c init_package.c -o init_package.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_abatch.c -o read_abatch.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_bpmap.c -o read_bpmap.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_cdf_xda.c -o read_cdf_xda.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_cdffile2.c -o read_cdffile2.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_celfile_generic.c -o read_celfile_generic.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_clf.c -o read_clf.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_generic.c -o read_generic.o
    read_generic.c:1288:42: warning: variable 'temp32' is uninitialized when used here [-Wuninitialized]
     Rprintf("Its a float value is %f\n",temp32);
     ^~~~~~
    read_generic.c:1278:13: note: initialize the variable 'temp32' to silence this warning
     int temp32;
     ^
     = 0
    1 warning generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -g -O2 -fPIC -Wall -g -O2 -c read_pgf.c -o read_pgf.o
    read_pgf.c:363:12: warning: unused function 'token_ends_with' [-Wunused-function]
    static int token_ends_with(char *token, char *ends_in){
     ^
    1 warning generated.
    clang -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 affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-affyio/00new/affyio/libs
    generating debug symbols (dSYM)
    ** R
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** 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 (affyio)
    * installing *source* package ‘preprocessCore’ ...
    ** using staged installation
    checking for gcc... clang
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether clang accepts -g... yes
    checking for clang option to accept ISO C89... none needed
    checking how to run the C preprocessor... clang -E
    checking for library containing pthread_create... none required
    checking for grep that handles long lines and -e... /usr/bin/grep
    checking for egrep... /usr/bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking for stdlib.h... (cached) yes
    checking if PTHREAD_STACK_MIN is defined... yes
    configure: Enabling threading for preprocessCore
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c R_colSummarize.c -o R_colSummarize.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c R_subColSummarize.c -o R_subColSummarize.o
    R_subColSummarize.c:99:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:97:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:105:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:103:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:267:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:265:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:271:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:273:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:438:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:436:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:444:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:442:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:616:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:614:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:610:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:608:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:785:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:781:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:779:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:787:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:959:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:957:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:953:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:951:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:1121:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:1123:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:1127:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:1129:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:1290:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer;
     ^
    R_subColSummarize.c:1292:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:1296:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:1298:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:1470:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:1472:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:1466:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:1639:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subColSummarize.c:1641:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subColSummarize.c:1639:30: warning: unused variable 'buffer2' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subColSummarize.c:1645:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subColSummarize.c:1647:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subColSummarize.c:1603:14: warning: unused function 'subColSummarize_medianpolish_group' [-Wunused-function]
    static void *subColSummarize_medianpolish_group(void *data){
     ^
    41 warnings generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o
    R_subrcModel_interfaces.c:79:11: warning: unused variable 'weights' [-Wunused-variable]
     double *weights;
     ^
    R_subrcModel_interfaces.c:80:11: warning: unused variable 'se' [-Wunused-variable]
     double *se;
     ^
    R_subrcModel_interfaces.c:64:20: warning: unused variable 'buffer2' [-Wunused-variable]
     double *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:64:11: warning: unused variable 'buffer' [-Wunused-variable]
     double *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:160:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subrcModel_interfaces.c:156:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    R_subrcModel_interfaces.c:162:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subrcModel_interfaces.c:154:30: warning: unused variable 'buffer2' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:154:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:154:11: warning: unused variable 'results' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:382:10: warning: unused variable 'scale' [-Wunused-variable]
     double scale=-1.0;
     ^
    R_subrcModel_interfaces.c:361:20: warning: unused variable 'buffer2' [-Wunused-variable]
     double *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:361:11: warning: unused variable 'buffer' [-Wunused-variable]
     double *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:469:11: warning: unused variable 'results' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:475:7: warning: unused variable 'ncur_rows' [-Wunused-variable]
     int ncur_rows;
     ^
    R_subrcModel_interfaces.c:477:9: warning: unused variable 'j' [-Wunused-variable]
     int i,j;
     ^
    R_subrcModel_interfaces.c:469:30: warning: unused variable 'buffer2' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:469:21: warning: unused variable 'buffer' [-Wunused-variable]
     double *results, *buffer, *buffer2;
     ^
    R_subrcModel_interfaces.c:471:8: warning: unused variable 'cur_rows' [-Wunused-variable]
     int *cur_rows;
     ^
    19 warnings generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c avg.c -o avg.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c avg_log.c -o avg_log.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c biweight.c -o biweight.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c init_package.c -o init_package.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c lm.c -o lm.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c log_avg.c -o log_avg.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c log_median.c -o log_median.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c median.c -o median.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c median_log.c -o median_log.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c medianpolish.c -o medianpolish.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c plmd.c -o plmd.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c plmr.c -o plmr.o
    plmr.c:82:13: warning: unused function 'XTWY_R' [-Wunused-function]
    static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){
     ^
    plmr.c:152:13: warning: unused function 'XTWX_R' [-Wunused-function]
    static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){
     ^
    plmr.c:279:13: warning: unused function 'XTWX_R_inv' [-Wunused-function]
    static void XTWX_R_inv(int *rows, int *cols, double *xtwx){
     ^
    3 warnings generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c psi_fns.c -o psi_fns.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c qnorm.c -o qnorm.o
    qnorm.c:1882:12: warning: unused variable 'j' [-Wunused-variable]
     size_t i,j,row_mean_ind;
     ^
    qnorm.c:1887:7: warning: unused variable 'non_na' [-Wunused-variable]
     int non_na;
     ^
    qnorm.c:2074:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
     } else if (isMatrix(target)){
     ^~~~~~~~~~~~~~~~
    /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1449:19: note: expanded from macro 'isMatrix'
    #define isMatrix Rf_isMatrix
     ^
    qnorm.c:2087:55: note: uninitialized use occurs here
     qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows);
     ^~~~~~~~~~~
    qnorm.c:2074:10: note: remove the 'if' if its condition is always true
     } else if (isMatrix(target)){
     ^~~~~~~~~~~~~~~~~~~~~
    qnorm.c:2055:21: note: initialize the variable 'target_rows' to silence this warning
     size_t target_rows, target_cols;
     ^
     = 0
    qnorm.c:2476:12: warning: unused variable 'j' [-Wunused-variable]
     size_t i,j,row_mean_ind;
     ^
    qnorm.c:2481:7: warning: unused variable 'non_na' [-Wunused-variable]
     int non_na;
     ^
    qnorm.c:2790:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
     double *sample_percentiles;
     ^
    qnorm.c:2791:11: warning: unused variable 'datvec' [-Wunused-variable]
     double *datvec;
     ^
    qnorm.c:2924:12: warning: unused variable 'j' [-Wunused-variable]
     size_t i,j,ind,target_ind;
     ^
    qnorm.c:2924:14: warning: unused variable 'ind' [-Wunused-variable]
     size_t i,j,ind,target_ind;
     ^
    qnorm.c:2924:18: warning: unused variable 'target_ind' [-Wunused-variable]
     size_t i,j,ind,target_ind;
     ^
    qnorm.c:2926:14: warning: unused variable 'dimat' [-Wunused-variable]
     dataitem **dimat;
     ^
    qnorm.c:2928:11: warning: unused variable 'row_mean' [-Wunused-variable]
     double *row_mean = target;
     ^
    qnorm.c:2930:11: warning: unused variable 'ranks' [-Wunused-variable]
     double *ranks = (double *)Calloc((rows),double);
     ^
    qnorm.c:2931:10: warning: unused variable 'samplepercentile' [-Wunused-variable]
     double samplepercentile;
     ^
    qnorm.c:2932:10: warning: unused variable 'target_ind_double' [-Wunused-variable]
     double target_ind_double,target_ind_double_floor;
     ^
    qnorm.c:2932:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable]
     double target_ind_double,target_ind_double_floor;
     ^
    qnorm.c:2934:7: warning: unused variable 'targetnon_na' [-Wunused-variable]
     int targetnon_na = targetrows;
     ^
    qnorm.c:2935:7: warning: unused variable 'non_na' [-Wunused-variable]
     int non_na = 0;
     ^
    qnorm.c:2939:11: warning: unused variable 'sample_percentiles' [-Wunused-variable]
     double *sample_percentiles;
     ^
    qnorm.c:2940:11: warning: unused variable 'datvec' [-Wunused-variable]
     double *datvec;
     ^
    qnorm.c:3191:14: warning: variable 'target_rows' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
     } else if (isMatrix(target)){
     ^~~~~~~~~~~~~~~~
    /Library/Frameworks/R.framework/Resources/include/Rinternals.h:1449:19: note: expanded from macro 'isMatrix'
    #define isMatrix Rf_isMatrix
     ^
    qnorm.c:3205:77: note: uninitialized use occurs here
     qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows);
     ^~~~~~~~~~~
    qnorm.c:3191:10: note: remove the 'if' if its condition is always true
     } else if (isMatrix(target)){
     ^~~~~~~~~~~~~~~~~~~~~
    qnorm.c:3172:21: note: initialize the variable 'target_rows' to silence this warning
     size_t target_rows, target_cols;
     ^
     = 0
    21 warnings generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c rlm.c -o rlm.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c rlm_anova.c -o rlm_anova.o
    rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable]
     double endprobe;
     ^
    rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable]
     double Kappa=0.0; /* A correction factor */
     ^
    rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable]
     double scale=0.0;
     ^
    rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable]
     double vs=0.0,m,varderivpsi=0.0;
     ^
    rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable]
     double sumderivpsi=0.0; /* sum of psi'(r_i) */
     ^
    rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable]
     double vs=0.0,m,varderivpsi=0.0;
     ^
    rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable]
     double sumpsi2=0.0; /* sum of psi(r_i)^2 */
     ^
    rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable]
     double vs=0.0,m,varderivpsi=0.0;
     ^
    rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable]
     double k1 = psi_k; /* was 1.345; */
     ^
    rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable]
     double endprobe;
     ^
    10 warnings generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c rlm_se.c -o rlm_se.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c rma_background4.c -o rma_background4.o
    rma_background4.c:342:10: warning: unused variable 'j' [-Wunused-variable]
     size_t j;
     ^
    rma_background4.c:343:10: warning: unused variable 'param' [-Wunused-variable]
     double param[3];
     ^
    2 warnings generated.
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c rma_common.c -o rma_common.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -Wall -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fPIC -Wall -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o
    clang -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 preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-preprocessCore/00new/preprocessCore/libs
    generating debug symbols (dSYM)
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** 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 (preprocessCore)
    * installing *source* package ‘limma’ ...
    ** using staged installation
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c normexp.c -o normexp.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c weighted_lowess.c -o weighted_lowess.o
    clang -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 limma.so init.o normexp.o weighted_lowess.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-limma/00new/limma/libs
    generating debug symbols (dSYM)
    ** R
    ** 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 (limma)
    * installing *source* package ‘affy’ ...
    ** using staged installation
    creating cache ./config.cache
    checking how to run the C preprocessor... cc -E
    checking for main in -lz... yes
    checking for zlib.h... yes
    checking if zlib version >= 1.1.3... yes
    updating cache ./config.cache
    creating ./config.status
    creating src/Makevars
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/preprocessCore/include" -I/usr/local/include -fPIC -Wall -g -O2 -c chipbackground.c -o chipbackground.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/preprocessCore/include" -I/usr/local/include -fPIC -Wall -g -O2 -c getall_locations.c -o getall_locations.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/preprocessCore/include" -I/usr/local/include -fPIC -Wall -g -O2 -c mas5calls.c -o mas5calls.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/preprocessCore/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rma2.c -o rma2.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/preprocessCore/include" -I/usr/local/include -fPIC -Wall -g -O2 -c rma_common.c -o rma_common.o
    clang -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 affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-affy/00new/affy/libs
    generating debug symbols (dSYM)
    ** 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 (affy)
    * installing *source* package ‘vsn’ ...
    ** using staged installation
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c vsn.c -o vsn.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c vsn2.c -o vsn2.o
    clang -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 vsn.so init.o vsn.o vsn2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brt.Rcheck/00LOCK-vsn/00new/vsn/libs
    generating debug symbols (dSYM)
    ** 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
    ** 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 (vsn)
    
    The downloaded source packages are in
     '/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmppy9lkq/downloaded_packages'
    
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.3.0
Check: PDF version of manual
Result: FAIL
    
Flavor: r-release-osx-x86_64

Version: 1.3.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘pasilla’
Flavor: r-oldrel-osx-x86_64