Error in re-building vignettes:
  ...
Loading required package: BiocInstaller
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'BiocInstaller'
Installing package into '/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb'
(as 'lib' is unspecified)
trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocInstaller_1.29.4.tar.gz'
Content type 'application/x-gzip' length 19160 bytes (18 KB)
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* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.7 (BiocInstaller 1.29.4), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
	'/tmp/Rtmpcoxm0i/downloaded_packages'
Bioconductor version 3.7 (BiocInstaller 1.29.4), ?biocLite for help
Loading required package: org.Hs.eg.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'org.Hs.eg.db'
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.29.4), R Under development
  (unstable) (2018-03-12 r74389).
Installing package(s) 'org.Hs.eg.db'
also installing the dependencies 'BiocGenerics', 'Biobase', 'IRanges', 'S4Vectors', 'AnnotationDbi'

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* installing *source* package ‘BiocGenerics’ ...
** 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 ‘lengths’ 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 ‘rowSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘colSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘rowMeans’ in package ‘BiocGenerics’
Creating a new generic function for ‘colMeans’ 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
* DONE (BiocGenerics)
* installing *source* package ‘Biobase’ ...
** libs
make[1]: Entering directory '/tmp/RtmpLBq6u5/R.INSTALL60ac649fdc5f/Biobase/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Rinit.c -o Rinit.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c anyMissing.c -o anyMissing.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c envir.c -o envir.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c matchpt.c -o matchpt.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c rowMedians.c -o rowMedians.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c sublist_extract.c -o sublist_extract.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o
make[1]: Leaving directory '/tmp/RtmpLBq6u5/R.INSTALL60ac649fdc5f/Biobase/src'
make[1]: Entering directory '/tmp/RtmpLBq6u5/R.INSTALL60ac649fdc5f/Biobase/src'
make[1]: Leaving directory '/tmp/RtmpLBq6u5/R.INSTALL60ac649fdc5f/Biobase/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Biobase/libs
** 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
* DONE (Biobase)
* installing *source* package ‘S4Vectors’ ...
** libs
make[1]: Entering directory '/tmp/RtmpxLUWlw/R.INSTALL72dc642798b7/S4Vectors/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c AEbufs.c -o AEbufs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c DataFrame_class.c -o DataFrame_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Hits_class.c -o Hits_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c LLint_class.c -o LLint_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c List_class.c -o List_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Rle_class.c -o Rle_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Rle_utils.c -o Rle_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c SEXP_utils.c -o SEXP_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c SimpleList_class.c -o SimpleList_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c anyMissing.c -o anyMissing.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c character_utils.c -o character_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c eval_utils.c -o eval_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c hash_utils.c -o hash_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c integer_utils.c -o integer_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c logical_utils.c -o logical_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c map_ranges_to_runs.c -o map_ranges_to_runs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c safe_arithm.c -o safe_arithm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -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"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c subsetting_utils.c -o subsetting_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c vector_utils.c -o vector_utils.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -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
make[1]: Leaving directory '/tmp/RtmpxLUWlw/R.INSTALL72dc642798b7/S4Vectors/src'
make[1]: Entering directory '/tmp/RtmpxLUWlw/R.INSTALL72dc642798b7/S4Vectors/src'
make[1]: Leaving directory '/tmp/RtmpxLUWlw/R.INSTALL72dc642798b7/S4Vectors/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘extractROWS’ with signature ‘"array","RangesNSBS"’: no definition for class “RangesNSBS”
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
* DONE (S4Vectors)
* installing *source* package ‘IRanges’ ...
** libs
make[1]: Entering directory '/tmp/RtmpohozeJ/R.INSTALL9c995a0f4e9b/IRanges/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c CompressedList_class.c -o CompressedList_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Grouping_class.c -o Grouping_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c IPosRanges_comparison.c -o IPosRanges_comparison.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c IRanges_class.c -o IRanges_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c IRanges_constructor.c -o IRanges_constructor.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -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"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c R_init_IRanges.c -o R_init_IRanges.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c Ranges_class.c -o Ranges_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c RleViews_utils.c -o RleViews_utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c coverage_methods.c -o coverage_methods.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/S4Vectors/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c inter_range_methods.c -o inter_range_methods.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -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 inter_range_methods.o
make[1]: Leaving directory '/tmp/RtmpohozeJ/R.INSTALL9c995a0f4e9b/IRanges/src'
make[1]: Entering directory '/tmp/RtmpohozeJ/R.INSTALL9c995a0f4e9b/IRanges/src'
make[1]: Leaving directory '/tmp/RtmpohozeJ/R.INSTALL9c995a0f4e9b/IRanges/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/IRanges/libs
** 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
* DONE (IRanges)
* installing *source* package ‘AnnotationDbi’ ...
** 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
* DONE (AnnotationDbi)
* installing *source* package ‘org.Hs.eg.db’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (org.Hs.eg.db)

The downloaded source packages are in
	'/tmp/Rtmpcoxm0i/downloaded_packages'
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
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Loading required package: IRanges
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Attaching package: 'S4Vectors'

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Loading required package: clusterProfiler
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
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BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.29.4), R Under development
  (unstable) (2018-03-12 r74389).
Installing package(s) 'clusterProfiler'
also installing the dependencies 'udunits2', 'tweenr', 'units', 'snow', 'data.table', 'fastmatch', 'ggforce', 'ggrepel', 'viridis', 'BiocParallel', 'DO.db', 'fgsea', 'cowplot', 'ggraph', 'DOSE', 'enrichplot', 'GO.db', 'GOSemSim', 'qvalue', 'rvcheck'

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* installing *source* package ‘udunits2’ ...
** package ‘udunits2’ successfully unpacked and MD5 sums checked
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 for XML_ParserCreate in -lexpat... yes
checking how to run the C preprocessor... clang -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 udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking for ut_read_xml in -ludunits2... yes
-----Error: udunits2.h not found-----
     If the udunits2 library is installed in a non-standard location,
     use --configure-args='--with-udunits2-lib=/usr/local/lib' for example,
     or --configure-args='--with-udunits2-include=/usr/include/udunits2'
     replacing paths with appropriate values for your installation.
     You can alternatively use the UDUNITS2_INCLUDE and UDUNITS2_LIB
     environment variables.
     If udunits2 is not installed, please install it.
     It is required for this package.
ERROR: configuration failed for package ‘udunits2’
* removing ‘/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/udunits2’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'udunits2' had non-zero exit status
* installing *source* package ‘tweenr’ ...
** package ‘tweenr’ successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/RtmpropkeZ/R.INSTALL5a3f34e09012/tweenr/src'
clang++ -std=gnu++98 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c RcppExports.cpp -o RcppExports.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c easing.c -o easing.o
clang++ -std=gnu++98 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c stateInterpolate.cpp -o stateInterpolate.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o tweenr.so RcppExports.o easing.o stateInterpolate.o
make[1]: Leaving directory '/tmp/RtmpropkeZ/R.INSTALL5a3f34e09012/tweenr/src'
make[1]: Entering directory '/tmp/RtmpropkeZ/R.INSTALL5a3f34e09012/tweenr/src'
make[1]: Leaving directory '/tmp/RtmpropkeZ/R.INSTALL5a3f34e09012/tweenr/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/tweenr/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (tweenr)
* installing *source* package ‘snow’ ...
** package ‘snow’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (snow)
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/RtmpOCluX5/R.INSTALL85c861136479/data.table/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c assign.c -o assign.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c between.c -o between.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c bmerge.c -o bmerge.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c chmatch.c -o chmatch.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c dogroups.c -o dogroups.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c fastmean.c -o fastmean.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c fcast.c -o fcast.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c fmelt.c -o fmelt.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c forder.c -o forder.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c frank.c -o frank.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c fread.c -o fread.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c fsort.c -o fsort.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c fwrite.c -o fwrite.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c gsumm.c -o gsumm.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c ijoin.c -o ijoin.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c init.c -o init.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c inrange.c -o inrange.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c openmp-utils.c -o openmp-utils.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c quickselect.c -o quickselect.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c rbindlist.c -o rbindlist.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c reorder.c -o reorder.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c shift.c -o shift.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c subset.c -o subset.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c transpose.c -o transpose.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c uniqlist.c -o uniqlist.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c vecseq.c -o vecseq.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include  -fopenmp -fpic  -g -O3 -Wall -pedantic  -c wrappers.c -o wrappers.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o dogroups.o fastmean.o fcast.o fmelt.o forder.o frank.o fread.o fsort.o fwrite.o gsumm.o ijoin.o init.o inrange.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o uniqlist.o vecseq.o wrappers.o -fopenmp
mv data.table.so datatable.so
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
make[1]: Leaving directory '/tmp/RtmpOCluX5/R.INSTALL85c861136479/data.table/src'
make[1]: Entering directory '/tmp/RtmpOCluX5/R.INSTALL85c861136479/data.table/src'
make[1]: Leaving directory '/tmp/RtmpOCluX5/R.INSTALL85c861136479/data.table/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/data.table/libs
** 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
* DONE (data.table)
* installing *source* package ‘fastmatch’ ...
** package ‘fastmatch’ successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/Rtmpc4F00m/R.INSTALLb07a41e61efe/fastmatch/src'
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c ctapply.c -o ctapply.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c fasthash.c -o fasthash.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c fastmatch.c -o fastmatch.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o fastmatch.so ctapply.o fasthash.o fastmatch.o
make[1]: Leaving directory '/tmp/Rtmpc4F00m/R.INSTALLb07a41e61efe/fastmatch/src'
make[1]: Entering directory '/tmp/Rtmpc4F00m/R.INSTALLb07a41e61efe/fastmatch/src'
make[1]: Leaving directory '/tmp/Rtmpc4F00m/R.INSTALLb07a41e61efe/fastmatch/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/fastmatch/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fastmatch)
* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/tmp/RtmpdEC2bf/R.INSTALLb3c2350bc938/ggrepel/src'
clang++ -std=gnu++98 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++98 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c repel_boxes.cpp -o repel_boxes.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o ggrepel.so RcppExports.o repel_boxes.o
make[1]: Leaving directory '/tmp/RtmpdEC2bf/R.INSTALLb3c2350bc938/ggrepel/src'
make[1]: Entering directory '/tmp/RtmpdEC2bf/R.INSTALLb3c2350bc938/ggrepel/src'
make[1]: Leaving directory '/tmp/RtmpdEC2bf/R.INSTALLb3c2350bc938/ggrepel/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/ggrepel/libs
** 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
* DONE (ggrepel)
* installing *source* package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (viridis)
* installing *source* package ‘DO.db’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (DO.db)
* installing *source* package ‘cowplot’ ...
** package ‘cowplot’ successfully unpacked and MD5 sums checked
** 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
* DONE (cowplot)
* installing *source* package ‘GO.db’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (GO.db)
* installing *source* package ‘qvalue’ ...
** 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
* DONE (qvalue)
* installing *source* package ‘rvcheck’ ...
** package ‘rvcheck’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rvcheck)
ERROR: dependency ‘udunits2’ is not available for package ‘units’
* removing ‘/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/units’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'units' had non-zero exit status
* installing *source* package ‘BiocParallel’ ...
** libs
make[1]: Entering directory '/tmp/RtmpC2Teiz/R.INSTALL456a2c6b08e0/BiocParallel/src'
clang++  -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/BH/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c ipcmutex.cpp -o ipcmutex.o
clang++ -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o BiocParallel.so ipcmutex.o
make[1]: Leaving directory '/tmp/RtmpC2Teiz/R.INSTALL456a2c6b08e0/BiocParallel/src'
make[1]: Entering directory '/tmp/RtmpC2Teiz/R.INSTALL456a2c6b08e0/BiocParallel/src'
make[1]: Leaving directory '/tmp/RtmpC2Teiz/R.INSTALL456a2c6b08e0/BiocParallel/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/BiocParallel/libs
** 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
* DONE (BiocParallel)
* installing *source* package ‘GOSemSim’ ...
** libs
make[1]: Entering directory '/tmp/RtmpVh7Zey/R.INSTALL55eb4181e03a/GOSemSim/src'
clang++ -std=gnu++98 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c ICmethod.cpp -o ICmethod.o
clang++ -std=gnu++98 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++98 -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o GOSemSim.so ICmethod.o RcppExports.o
make[1]: Leaving directory '/tmp/RtmpVh7Zey/R.INSTALL55eb4181e03a/GOSemSim/src'
make[1]: Entering directory '/tmp/RtmpVh7Zey/R.INSTALL55eb4181e03a/GOSemSim/src'
make[1]: Leaving directory '/tmp/RtmpVh7Zey/R.INSTALL55eb4181e03a/GOSemSim/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/GOSemSim/libs
** 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
* DONE (GOSemSim)
ERROR: dependency ‘units’ is not available for package ‘ggforce’
* removing ‘/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/ggforce’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'ggforce' had non-zero exit status
* installing *source* package ‘fgsea’ ...
** libs
make[1]: Entering directory '/tmp/RtmpFi9snY/R.INSTALL76e53389181c/fgsea/src'
clang++  -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c RcppExports.cpp -o RcppExports.o
clang++  -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic -frtti -c fastGSEA.cpp -o fastGSEA.o
clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I"/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/Rcpp/include" -isystem /usr/local/clang/include   -fpic  -g -O3 -Wall -pedantic  -c fgsea_init.c -o fgsea_init.o
clang++ -shared -L/usr/local/clang/lib64 -L/usr/local/lib64 -o fgsea.so RcppExports.o fastGSEA.o fgsea_init.o
make[1]: Leaving directory '/tmp/RtmpFi9snY/R.INSTALL76e53389181c/fgsea/src'
make[1]: Entering directory '/tmp/RtmpFi9snY/R.INSTALL76e53389181c/fgsea/src'
make[1]: Leaving directory '/tmp/RtmpFi9snY/R.INSTALL76e53389181c/fgsea/src'
installing to /tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/fgsea/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (fgsea)
ERROR: dependency ‘ggforce’ is not available for package ‘ggraph’
* removing ‘/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/ggraph’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'ggraph' had non-zero exit status
* installing *source* package ‘DOSE’ ...
** 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
* DONE (DOSE)
ERROR: dependency ‘ggraph’ is not available for package ‘enrichplot’
* removing ‘/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/enrichplot’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'enrichplot' had non-zero exit status
ERROR: dependency ‘enrichplot’ is not available for package ‘clusterProfiler’
* removing ‘/tmp/Rtmp8SHOmD/RLIBS_1db25cf556bb/clusterProfiler’
Warning in install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'clusterProfiler' had non-zero exit status

The downloaded source packages are in
	'/tmp/Rtmpcoxm0i/downloaded_packages'
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: readxl
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.21.0 (2016-10-30) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:igraph':

    hierarchy

The following object is masked from 'package:IRanges':

    trim

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

R.utils v2.6.0 (2017-11-04) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings


Quitting from lines 42-51 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
Execution halted