Back to Multiple platform build/check report for BioC 3.11
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

INSTALL report for IRanges on tokay2

This page was generated on 2020-10-17 11:56:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IRanges PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 894/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.22.2
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/IRanges
Branch: RELEASE_3_11
Last Commit: 8c5e991
Last Changed Date: 2020-05-20 17:05:42 -0400 (Wed, 20 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.22.2
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/IRanges_2.22.2.tar.gz && rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRanges.buildbin-libdir IRanges_2.22.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL IRanges_2.22.2.zip && rm IRanges_2.22.2.tar.gz IRanges_2.22.2.zip
StartedAt: 2020-10-16 16:58:24 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:01:25 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 180.9 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/IRanges_2.22.2.tar.gz && rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRanges.buildbin-libdir IRanges_2.22.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL IRanges_2.22.2.zip && rm IRanges_2.22.2.tar.gz IRanges_2.22.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  265k  100  265k    0     0  3340k      0 --:--:-- --:--:-- --:--:-- 3631k

install for i386

* installing *source* package 'IRanges' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedList_class.c -o CompressedList_class.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Grouping_class.c -o Grouping_class.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IPosRanges_comparison.c -o IPosRanges_comparison.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_class.c -o IRanges_class.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_constructor.c -o IRanges_constructor.o
IRanges_constructor.c: In function 'solve_range':
IRanges_constructor.c:43:22: warning: unknown conversion type character 'l' in format [-Wformat=]
      "the 'width' (%lld) inferred from the "
                      ^
IRanges_constructor.c:43:6: warning: too many arguments for format [-Wformat-extra-args]
      "the 'width' (%lld) inferred from the "
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:66:22: warning: unknown conversion type character 'l' in format [-Wformat=]
      "the 'start' (%lld) inferred from the "
                      ^
IRanges_constructor.c:66:6: warning: too many arguments for format [-Wformat-extra-args]
      "the 'start' (%lld) inferred from the "
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:86:20: warning: unknown conversion type character 'l' in format [-Wformat=]
      "the 'end' (%lld) inferred from the "
                    ^
IRanges_constructor.c:86:6: warning: too many arguments for format [-Wformat-extra-args]
      "the 'end' (%lld) inferred from the "
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:98:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     "the supplied 'width' (%d) doesn't match "
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:100:27: note: format string is defined here
     "'start' and 'end' (%lld)", width, tmp);
                           ^
IRanges_constructor.c:98:5: warning: too many arguments for format [-Wformat-extra-args]
     "the supplied 'width' (%d) doesn't match "
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NCList.c -o NCList.o
NCList.c:1173:13: 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:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^~~~~~~~~~~~~
NCList.c: In function 'NCListAsINTSXP_print':
NCList.c:674:23: warning: '%d' directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=]
   sprintf(format, "%c0%d%c", '%', max_digits, 'd');
                       ^~
NCList.c:674:19: note: directive argument in the range [-2147483647, 2147483647]
   sprintf(format, "%c0%d%c", '%', max_digits, 'd');
                   ^~~~~~~~~
NCList.c:674:3: note: 'sprintf' output between 5 and 15 bytes into a destination of size 10
   sprintf(format, "%c0%d%c", '%', max_digits, 'd');
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1546:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_IRanges.c -o R_init_IRanges.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Ranges_class.c -o Ranges_class.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RleViews_utils.c -o RleViews_utils.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                     ^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'find_partition_overlaps':
extractListFragments.c:66:5: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(split_partitions_buf,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      IntAE_get_nelt(split_partitions_buf),
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      q_prev_end);
      ~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inter_range_methods.c -o inter_range_methods.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/libs/i386
** 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 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' 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'
Creating a generic function for 'startsWith' from package 'base' in package 'IRanges'
Creating a generic function for 'endsWith' from package 'base' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a new generic function for 'windows' in package 'IRanges'
** help
*** installing help indices
  converting help for package 'IRanges'
    finding HTML links ... done
    AtomicList-class                        html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/AtomicList-class.Rd:307: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    AtomicList-utils                        html  
    CompressedHitsList-class                html  
    CompressedList-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:38: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:39: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:44: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:50: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:60: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:66: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:81: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:84: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:87: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:89: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:95: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:100: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:105: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:110: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:118: file link 'classNameForDisplay' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:124: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/CompressedList-class.Rd:127: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
    DataFrame-utils                         html  
    DataFrameList-class                     html  
    Grouping-class                          html  
    Hits-class-leftovers                    html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Hits-class-leftovers.Rd:31: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Hits-class-leftovers.Rd:68: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    IPos-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPos-class.Rd:122: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPos-class.Rd:192: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPos-class.Rd:209: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
    IPosRanges-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPosRanges-class.Rd:198: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPosRanges-class.Rd:223: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPosRanges-class.Rd:223: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPosRanges-class.Rd:224: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPosRanges-class.Rd:224: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPosRanges-class.Rd:225: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    IPosRanges-comparison                   html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IPosRanges-comparison.Rd:164: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    IRanges-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IRanges-class.Rd:97: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IRanges-class.Rd:120: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    IRanges-constructor                     html  
    IRanges-internals                       html  
    IRanges-utils                           html  
    IRangesList-class                       html  
    IntegerRanges-class                     html  
    IntegerRangesList-class                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IntegerRangesList-class.Rd:76: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IntegerRangesList-class.Rd:76: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IntegerRangesList-class.Rd:77: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/IntegerRangesList-class.Rd:77: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    List-class-leftovers                    html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/List-class-leftovers.Rd:11: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/List-class-leftovers.Rd:35: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    MaskCollection-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/MaskCollection-class.Rd:206: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
    NCList-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:81: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:101: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:102: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:110: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:126: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:128: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:131: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/NCList-class.Rd:155: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    RangedData-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/RangedData-class.Rd:62: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/RangedData-class.Rd:63: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/RangedData-class.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/RangedData-class.Rd:65: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/RangedData-class.Rd:69: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/RangedData-class.Rd:70: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    RangedSelection-class                   html  
    Rle-class-leftovers                     html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Rle-class-leftovers.Rd:22: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Rle-class-leftovers.Rd:71: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
    RleViews-class                          html  
    RleViewsList-class                      html  
    Vector-class-leftovers                  html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Vector-class-leftovers.Rd:29: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Vector-class-leftovers.Rd:109: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
    Views-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Views-class.Rd:48: file link 'XIntegerViews' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Views-class.Rd:49: file link 'XStringViews' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/Views-class.Rd:158: file link 'XVector' in package 'XVector' does not exist and so has been treated as a topic
    ViewsList-class                         html  
    coverage-methods                        html  
    extractList                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:79: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:129: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:140: file link 'unsplit' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:143: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:146: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:146: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:147: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:147: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:149: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractList.Rd:150: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    extractListFragments                    html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractListFragments.Rd:78: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractListFragments.Rd:79: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractListFragments.Rd:80: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractListFragments.Rd:87: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractListFragments.Rd:104: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractListFragments.Rd:104: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/extractListFragments.Rd:107: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    findOverlaps-methods                    html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:56: file link 'findOverlaps,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:58: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:169: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:177: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:189: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:189: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:247: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:247: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:255: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:256: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:287: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:287: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:291: file link 'findOverlaps,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:293: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/findOverlaps-methods.Rd:293: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    inter-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/inter-range-methods.Rd:266: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
    intra-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:94: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:102: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:123: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:136: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:146: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:160: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:188: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:251: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:252: file link 'promoters,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:297: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/intra-range-methods.Rd:307: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
    multisplit                              html  
    nearest-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/nearest-methods.Rd:148: file link 'breakTies' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/nearest-methods.Rd:174: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/nearest-methods.Rd:175: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/nearest-methods.Rd:188: file link 'precede,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
    range-squeezers                         html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:15: file link 'granges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:16: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:19: file link 'granges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:20: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:21: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:32: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:33: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:34: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:35: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:36: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:37: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:64: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:77: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:93: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:96: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:97: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/range-squeezers.Rd:98: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    read.Mask                               html  
    reverse-methods                         html  
    seqapply                                html  
    setops-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/setops-methods.Rd:91: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/setops-methods.Rd:116: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMLfBHX/R.INSTALLf08636e7910/IRanges/man/setops-methods.Rd:165: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
    slice-methods                           html  
    view-summarization-methods              html  
** 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

install for x64

* installing *source* package 'IRanges' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedList_class.c -o CompressedList_class.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Grouping_class.c -o Grouping_class.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IPosRanges_comparison.c -o IPosRanges_comparison.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_class.c -o IRanges_class.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_constructor.c -o IRanges_constructor.o
IRanges_constructor.c: In function 'solve_range':
IRanges_constructor.c:43:22: warning: unknown conversion type character 'l' in format [-Wformat=]
      "the 'width' (%lld) inferred from the "
                      ^
IRanges_constructor.c:43:6: warning: too many arguments for format [-Wformat-extra-args]
      "the 'width' (%lld) inferred from the "
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:66:22: warning: unknown conversion type character 'l' in format [-Wformat=]
      "the 'start' (%lld) inferred from the "
                      ^
IRanges_constructor.c:66:6: warning: too many arguments for format [-Wformat-extra-args]
      "the 'start' (%lld) inferred from the "
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:86:20: warning: unknown conversion type character 'l' in format [-Wformat=]
      "the 'end' (%lld) inferred from the "
                    ^
IRanges_constructor.c:86:6: warning: too many arguments for format [-Wformat-extra-args]
      "the 'end' (%lld) inferred from the "
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:98:5: warning: unknown conversion type character 'l' in format [-Wformat=]
     "the supplied 'width' (%d) doesn't match "
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IRanges_constructor.c:100:27: note: format string is defined here
     "'start' and 'end' (%lld)", width, tmp);
                           ^
IRanges_constructor.c:98:5: warning: too many arguments for format [-Wformat-extra-args]
     "the supplied 'width' (%d) doesn't match "
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NCList.c -o NCList.o
NCList.c:1173:13: 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:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^~~~~~~~~~~~~
NCList.c: In function 'NCListAsINTSXP_print':
NCList.c:674:23: warning: '%d' directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=]
   sprintf(format, "%c0%d%c", '%', max_digits, 'd');
                       ^~
NCList.c:674:19: note: directive argument in the range [-2147483647, 2147483647]
   sprintf(format, "%c0%d%c", '%', max_digits, 'd');
                   ^~~~~~~~~
NCList.c:674:3: note: 'sprintf' output between 5 and 15 bytes into a destination of size 10
   sprintf(format, "%c0%d%c", '%', max_digits, 'd');
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_IRanges.c -o R_init_IRanges.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Ranges_class.c -o Ranges_class.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RleViews_utils.c -o RleViews_utils.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
                     ^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'find_partition_overlaps':
extractListFragments.c:66:5: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(split_partitions_buf,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      IntAE_get_nelt(split_partitions_buf),
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      q_prev_end);
      ~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inter_range_methods.c -o inter_range_methods.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.22.2.zip
* DONE (IRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'IRanges' successfully unpacked and MD5 sums checked