Package: XVector

Version: 0.20.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XVector.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings XVector_0.20.0.tar.gz

StartedAt: 2018-10-17 05:27:32 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 05:29:15 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 103.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: XVector.Rcheck

Warnings: 3

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XVector.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings XVector_0.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/XVector.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'XVector/DESCRIPTION' ... OK
* this is package 'XVector' version '0.20.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'XVector' can be installed ... WARNING
Found the following significant warnings:
  RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args]
  RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args]
  RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args]
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XDoubleViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XDoubleViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XDoubleViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XIntegerViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XIntegerViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XIntegerViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XRawList-comparison.Rd:106: missing file link 'Ranges-comparison'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XVector-class.Rd:58: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XVector-class.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XVector-class.Rd:134: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:19: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:19: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:38: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:65: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/reverse-methods.Rd:48: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/slice-methods.Rd:14: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/slice-methods.Rd:53: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/XVector.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'S4Vectors' 'IRanges'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'BiocGenerics:::testPackage'
  'IRanges:::new_Views' 'IRanges:::solveUserSEWForSingleSeq'
  'S4Vectors:::anyMissing' 'S4Vectors:::prepare_objects_to_concatenate'
  'S4Vectors:::setDefaultSlotValue' 'S4Vectors:::toNumSnippet'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'XRawList-comparison.Rd':
  '[IRanges]{Ranges-comparison}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'RdaCollection' 'rdaPath'
Undocumented S4 classes:
  'RdaCollection'
Undocumented S4 methods:
  generic '[[' and siglist 'RdaCollection'
  generic 'coerce' and siglist 'XVector,Rle'
  generic 'extractList' and siglist 'XVector,IntegerRanges'
  generic 'length' and siglist 'RdaCollection'
  generic 'names' and siglist 'RdaCollection'
  generic 'rdaPath' and siglist 'RdaCollection'
  generic 'relist' and siglist 'XVector,PartitioningByEnd'
  generic 'relistToClass' and siglist 'XVector'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/libs/i386/XVector.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/XVector.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/XVector_0.20.0.tar.gz && rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XVector.buildbin-libdir XVector_0.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL XVector_0.20.0.zip && rm XVector_0.20.0.tar.gz XVector_0.20.0.zip
###
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install for i386

* installing *source* package 'XVector' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function 'RDS_read_character_vector':
RDS_random_access.c:305:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_atomic_vector':
RDS_random_access.c:335:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_list':
RDS_random_access.c:379:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_extract_subarray':
RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
  SEXP subscript, ans;
                  ^
RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable]
  SEXPTYPE x_type;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_XVector.c -o R_init_XVector.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedDouble_class.c -o SharedDouble_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedInteger_class.c -o SharedInteger_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript':
SharedRaw_class.c:350:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
  SEXP dest, src_tag;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedVector_class.c -o SharedVector_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XRawList_comparison.c -o XRawList_comparison.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:452:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
   ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_class.c -o XVector_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c io_utils.c -o io_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c slice_methods.c -o slice_methods.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vector_copy.c -o vector_copy.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function 'get_which_min_from_Ints_holder':
view_summarization_methods.c:219:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder':
view_summarization_methods.c:246:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Ints_holder':
view_summarization_methods.c:269:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder':
view_summarization_methods.c:296:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/XVector.buildbin-libdir/XVector/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'XVector'
    finding HTML links ... done
    OnDiskRaw-class                         html  
    XDoubleViews-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XDoubleViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XDoubleViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XDoubleViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
    XIntegerViews-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XIntegerViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XIntegerViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XIntegerViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
    XRawList-class                          html  
    XRawList-comparison                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XRawList-comparison.Rd:106: missing file link 'Ranges-comparison'
    XVector-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XVector-class.Rd:58: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XVector-class.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/XVector-class.Rd:134: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
    XVector-internals                       html  
    XVectorList-class                       html  
    compact-methods                         html  
    intra-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:19: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:19: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:38: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/intra-range-methods.Rd:65: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
    reverse-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/reverse-methods.Rd:48: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
    slice-methods                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/slice-methods.Rd:14: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuS2iL0/R.INSTALL16241cda3973/XVector/man/slice-methods.Rd:53: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    updateObject-methods                    html  
    view-summarization-methods              html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'XVector' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function 'RDS_read_character_vector':
RDS_random_access.c:305:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_atomic_vector':
RDS_random_access.c:335:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_list':
RDS_random_access.c:379:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_extract_subarray':
RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
  SEXP subscript, ans;
                  ^
RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable]
  SEXPTYPE x_type;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_XVector.c -o R_init_XVector.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedDouble_class.c -o SharedDouble_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedInteger_class.c -o SharedInteger_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript':
SharedRaw_class.c:350:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
  SEXP dest, src_tag;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedVector_class.c -o SharedVector_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XRawList_comparison.c -o XRawList_comparison.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:452:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_class.c -o XVector_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c io_utils.c -o io_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c slice_methods.c -o slice_methods.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vector_copy.c -o vector_copy.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function 'get_which_min_from_Ints_holder':
view_summarization_methods.c:219:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder':
view_summarization_methods.c:246:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Ints_holder':
view_summarization_methods.c:269:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder':
view_summarization_methods.c:296:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/XVector.buildbin-libdir/XVector/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'XVector' as XVector_0.20.0.zip
* DONE (XVector)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'XVector' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("XVector") || stop("unable to load XVector package")
Loading required package: XVector
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

[1] TRUE
> XVector:::.test()


RUNIT TEST PROTOCOL -- Wed Oct 17 05:29:05 2018 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
XVector RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.56    0.14    2.71 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("XVector") || stop("unable to load XVector package")
Loading required package: XVector
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

[1] TRUE
> XVector:::.test()


RUNIT TEST PROTOCOL -- Wed Oct 17 05:29:09 2018 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
XVector RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   3.45    0.28    3.78