Package: IRanges

Version: 1.14.1

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_1.14.1.tar.gz

StartedAt: 2012-04-01 01:45:51 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:48:07 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 136.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IRanges.Rcheck

Warnings: 3

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/IRanges.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.14.1'
* 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 whether package 'IRanges' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mcseqapply: no visible global function definition for 'mclapply'
Found .Internal calls in the following functions:
  'isNotSorted' 'isNotStrictlySorted'
with calls to .Internal functions
  'is.unsorted'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/IRanges.Rcheck/00_pkg_src/IRanges/man/encodeOverlaps.Rd':
  'Hits'

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

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'encodeOverlaps':
encodeOverlaps
  Code: function(query, subject, hits = NULL, ...)
  Docs: function(query, subject, hits = NULL)
  Argument names in code not in docs:
    ...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: 'BSgenome.Celegans.UCSC.ce2'
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/IRanges.Rcheck/IRanges/libs/IRanges.so':
  Found 'abort', possibly from 'abort' (C)
    Object: 'errabort.o'
  Found 'exit', possibly from 'exit' (C)
    Object: 'errabort.o'
  Found 'stderr', possibly from 'stderr' (C)
    Object: 'errabort.o'
  Found 'stdout', possibly from 'stdout' (C)
    Objects: 'IntervalTree.o', 'common.o', 'errabort.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'IRanges_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/IRanges.Rcheck/00check.log'
for details.

* installing *source* package 'IRanges' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Hits_class.c -o Hits_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c IRanges_utils.c -o IRanges_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c IntervalTree.c -o IntervalTree.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rle_utils.c -o Rle_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SharedDouble_utils.c -o SharedDouble_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SharedInteger_utils.c -o SharedInteger_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SharedRaw_utils.c -o SharedRaw_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Vector_class.c -o Vector_class.o
Vector_class.c: In function 'vector_seqselect':
Vector_class.c:95:4: warning: implicit declaration of function 'UNIMPLEMENTED_TYPE' [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c XDoubleViews_utils.c -o XDoubleViews_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c XVectorList_class.c -o XVectorList_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c common.c -o common.o
common.c: In function 'firstWordInFile':
common.c:1787:6: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coverage.c -o coverage.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c encode_overlaps.c -o encode_overlaps.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c int_utils.c -o int_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c memalloc.c -o memalloc.o
memalloc.c: In function 'carefulAlloc':
memalloc.c:293:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:293:2: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' [-Wformat]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ucsc_handlers.c -o ucsc_handlers.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -shared -L/usr/local/lib -o IRanges.so AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IRanges_utils.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_utils.o SharedInteger_utils.o SharedRaw_utils.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o XIntegerViews_utils.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage.o dlist.o encode_overlaps.o errabort.o int_utils.o localmem.o memalloc.o rbTree.o sort_utils.o str_utils.o ucsc_handlers.o vector_copy.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nlevels' from package 'base' in package 'IRanges'
Creating a generic function for 'window' from package 'stats' in package 'IRanges'
Creating a generic function for 'window<-' from package 'stats' in package 'IRanges'
Creating a generic function for 'head' from package 'utils' in package 'IRanges'
Creating a generic function for 'tail' from package 'utils' in package 'IRanges'
Creating a generic function for 'rev' from package 'base' in package 'IRanges'
Creating a generic function for 'subset' from package 'base' in package 'IRanges'
Creating a generic function for 'as.data.frame' from package 'base' in package 'IRanges'
Creating a generic function for 'append' from package 'base' in package 'IRanges'
Creating a generic function for 'split<-' from package 'base' in package 'IRanges'
Creating a generic function for 'aggregate' from package 'stats' in package 'IRanges'
Creating a generic function for 'as.list' from package 'base' in package 'IRanges'
Creating a generic function for 'stack' from package 'utils' in package 'IRanges'
Creating a generic function for 'relist' from package 'utils' in package 'IRanges'
Creating a generic function for 'unsplit' from package 'base' in package 'IRanges'
Creating a generic function for 'with' from package 'base' in package 'IRanges'
Creating a generic function for 'within' from package 'base' in package 'IRanges'
Creating a generic function for 'start' from package 'stats' in package 'IRanges'
Creating a generic function for 'end' from package 'stats' in package 'IRanges'
Creating a generic function for 'update' from package 'stats' in package 'IRanges'
Creating a generic function for 'as.matrix' from package 'base' in package 'IRanges'
Creating a generic function for 'unlist' from package 'base' in package 'IRanges'
Creating a generic function for 'sort' from package 'base' in package 'IRanges'
Creating a generic function for 'rank' from package 'base' in package 'IRanges'
Creating a generic function for '%in%' from package 'base' in package 'IRanges'
Creating a generic function for 'na.omit' from package 'stats' in package 'IRanges'
Creating a generic function for 'na.exclude' from package 'stats' in package 'IRanges'
Creating a generic function for 'complete.cases' from package 'stats' in package 'IRanges'
Creating a generic function for 'merge' from package 'base' 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 'as.vector' from package 'base' in package 'IRanges'
Creating a generic function for 'as.factor' from package 'base' in package 'IRanges'
Creating a generic function for 'is.unsorted' from package 'base' in package 'IRanges'
Creating a generic function for 'split' 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 'var' from package 'stats' in package 'IRanges'
Creating a generic function for 'cov' from package 'stats' in package 'IRanges'
Creating a generic function for 'cor' from package 'stats' in package 'IRanges'
Creating a generic function for 'sd' from package 'stats' 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 'mad' from package 'stats' in package 'IRanges'
Creating a generic function for 'IQR' 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 'nchar' from package 'base' in package 'IRanges'
Creating a generic function for 'substr' from package 'base' in package 'IRanges'
Creating a generic function for 'substring' from package 'base' 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'
Creating a generic function for 'levels' from package 'base' in package 'IRanges'
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'rownames<-' from package 'base' in package 'IRanges'
Creating a generic function for 'colnames<-' from package 'base' in package 'IRanges'
Creating a generic function for 'as.table' from package 'base' in package 'IRanges'
Creating a generic function for 't' from package 'base' in package 'IRanges'
Creating a generic function for 'toString' from package 'base' in package 'IRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
   'IRangesOverview.Rnw' 
   'RleTricks.Rnw' 
** testing if installed package can be loaded

* DONE (IRanges)

name	user	system	elapsed
AtomicList-class	0.320	0.004	0.321
DataFrame-class	0.324	0.008	0.333
DataTable-API	0.000	0.000	0.001
DataTable-stats	0.004	0.004	0.010
FilterRules-class	0.028	0.000	0.026
GappedRanges-class	0.120	0.004	0.123
Grouping-class	0.056	0.000	0.056
Hits-class	0.020	0.000	0.019
IRanges-class	1.060	0.116	1.177
IRanges-constructor	0.036	0.000	0.037
IRanges-setops	0.108	0.000	0.107
IRanges-utils	1.160	0.112	1.274
IRangesList-class	0.036	0.000	0.035
IntervalTree-class	0.204	0.000	0.204
List-class	0.004	0.000	0.004
MaskCollection-class	0.124	0.000	0.125
OverlapEncodings-class	0.036	0.000	0.046
RDApplyParams-class	0.496	0.004	0.495
RangedData-class	1.100	0.008	1.107
RangedData-utils	0.064	0.000	0.063
RangedDataList-class	0.028	0.000	0.029
RangedSelection-class	0.016	0.000	0.015
Ranges-class	0.048	0.000	0.047
Ranges-comparison	0.024	0.000	0.025
Ranges-utils	0.092	0.000	0.092
RangesList-class	0.056	0.000	0.058
RangesList-utils	0.296	0.004	0.303
Rle-class	0.076	0.000	0.077
RleViews-class	0.036	0.000	0.035
RleViewsList-class	0.040	0.000	0.042
SimpleList-class	0.004	0.000	0.004
Vector-class	0.004	0.000	0.004
Views-class	0.22	0.00	0.22
Views-utils	0.04	0.00	0.04
ViewsList-class	0.000	0.000	0.001
XDoubleViews-class	0.040	0.000	0.044
XIntegerViews-class	0.028	0.000	0.031
XVector-class	0.032	0.000	0.030
compact	0.308	0.000	0.312
coverage	0.06	0.00	0.06
disjoin	0.012	0.000	0.012
encodeOverlaps	0.016	0.000	0.019
endoapply	0.004	0.000	0.007
isConstant	0.000	0.000	0.002
multisplit	0.024	0.000	0.024
nearest	0.020	0.000	0.022
read.Mask	0.044	0.004	0.049
reverse	0.052	0.000	0.052
runstat	0.024	0.000	0.024
seqapply	0.044	0.000	0.043
strutils	0	0	0