I am trying to install IRanges in R 3.3 with bioconductor 3.3.

The error message is here:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("IRanges")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘IRanges’
trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/IRanges_2.6.1.tar.gz'
Content type 'application/x-gzip' length 475440 bytes (464 KB)
==================================================
downloaded 464 KB

* installing *source* package ‘IRanges’ ...
** libs
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c CompressedList_class.c -o CompressedList_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c GappedRanges_class.c -o GappedRanges_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c Grouping_class.c -o Grouping_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c IRanges_class.c -o IRanges_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c NCList.c -o NCList.o
NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^
NCList.c:1184:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
 static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
             ^
NCList.c: In function ‘NCList_find_overlaps_in_groups’:
NCList.c:1553:7: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c Ranges_class.c -o Ranges_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c Ranges_comparison.c -o Ranges_comparison.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c RleViews_utils.c -o RleViews_utils.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:503:28: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (*out_ranges_are_tiles && x_end != cvg_len)
                            ^
coverage_methods.c:419:21: note: ‘x_end’ was declared here
      i, j, x_start, x_end, shift_elt, tmp;
                     ^
gcc -m64 -I/usr/include/R -DNDEBUG  -I/usr/local/include -I"/usr/lib64/R/library/S4Vectors/include"   -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic  -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function ‘reduce_ranges’:
inter_range_methods.c:165:5: warning: ‘revmap_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(revmap_elt,
     ^
inter_range_methods.c:154:11: warning: ‘delta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
inter_range_methods.c:154:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
inter_range_methods.c:156:14: warning: ‘max_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    width_inc = end_j - max_end;
              ^
inter_range_methods.c:131:6: warning: ‘append_or_drop’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (append_or_drop) {
      ^
gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -L/usr/lib64/R/lib -lR
installing to /home/jl/R/x86_64-redhat-linux-gnu-library/3.3/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ 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’
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) : 
  methods can add arguments to the generic ‘NSBS’ only if '...' is an argument to the generic
Error : unable to load R code in package ‘IRanges’
ERROR: lazy loading failed for package ‘IRanges’
* removing ‘/home/jl/R/x86_64-redhat-linux-gnu-library/3.3/IRanges’

The downloaded source packages are in
    ‘/tmp/RtmpnK0JTG/downloaded_packages’
Old packages: 'AnnotationDbi', 'biomaRt', 'Biostrings', 'BSgenome', 'CNEr',
  'DirichletMultinomial', 'GenomeInfoDb', 'GenomicAlignments',
  'GenomicFeatures', 'GenomicRanges', 'IRanges', 'Rsamtools', 'rtracklayer',
  'ShortRead', 'SummarizedExperiment', 'TFBSTools', 'XVector'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IRanges’ had non-zero exit status

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 23 (Workstation Edition)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] tools_3.3.1

This looks like a package version mismatch error. Try running BiocInstaller::biocValid() and following directions about too new / too old packages.