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Package 263/514HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.12.6
Bioconductor Package Maintainer
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/IRanges
Last Changed Rev: 62588 / Revision: 64395
Last Changed Date: 2012-02-06 13:54:38 -0800 (Mon, 06 Feb 2012)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: IRanges
Version: 1.12.6
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_1.12.6.tar.gz
StartedAt: 2012-03-24 01:06:10 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:09:09 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 178.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘1.12.6’
* 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’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'as.data.frame' and siglist 'Vector'
  generic 'coerce' and siglist 'Vector,data.frame'
  generic 'slice' and siglist 'numeric'
  generic 'unique' and siglist 'Vector'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 ... NOTE
‘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/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/IRanges/libs/IRanges.so’:
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  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 ... 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 was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/00check.log’
for details

IRanges.Rcheck/00install.out:

* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c IRanges_utils.c -o IRanges_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c IntervalTree.c -o IntervalTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rle_utils.c -o Rle_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SharedDouble_utils.c -o SharedDouble_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SharedInteger_utils.c -o SharedInteger_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SharedRaw_utils.c -o SharedRaw_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -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’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c XDoubleViews_utils.c -o XDoubleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c XVectorList_class.c -o XVectorList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c coverage.c -o coverage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c int_utils.c -o int_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c memalloc.c -o memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o IRanges.so AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o IRanges_utils.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.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 errabort.o int_utils.o localmem.o memalloc.o rbTree.o sort_utils.o str_utils.o vector_copy.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘NROW’ from package ‘base’ in package ‘IRanges’
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 new generic function for ‘rep.int’ in package ‘IRanges’
Creating a generic function for ‘subset’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘unique’ 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 ‘tapply’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sapply’ from package ‘base’ in package ‘IRanges’
Creating a new generic function for ‘mapply’ 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 ‘Reduce’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘Filter’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘Find’ from package ‘base’ in package ‘IRanges’
Creating a new generic function for ‘Map’ in package ‘IRanges’
Creating a generic function for ‘Position’ from package ‘base’ in package ‘IRanges’
Creating a new generic function for ‘eval’ in package ‘IRanges’
Creating a generic function for ‘with’ 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 ‘duplicated’ from package ‘base’ in package ‘IRanges’
Creating a new generic function for ‘order’ 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 new generic function for ‘union’ in package ‘IRanges’
Creating a new generic function for ‘intersect’ in package ‘IRanges’
Creating a new generic function for ‘setdiff’ in package ‘IRanges’
Creating a generic function for ‘NCOL’ 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 new generic function for ‘cbind’ in package ‘IRanges’
Creating a new generic function for ‘rbind’ in package ‘IRanges’
Creating a generic function for ‘xtabs’ from package ‘stats’ 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 ‘summary’ from package ‘base’ in package ‘IRanges’
Creating a new generic function for ‘table’ 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 new generic function for ‘pmax’ in package ‘IRanges’
Creating a new generic function for ‘pmin’ in package ‘IRanges’
Creating a new generic function for ‘pmax.int’ in package ‘IRanges’
Creating a new generic function for ‘pmin.int’ 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 new generic function for ‘paste’ in package ‘IRanges’
Creating a generic function for ‘levels’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘ncol’ 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 ‘rownames<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘within’ 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 ...
*** tangling vignette sources ...
   ‘IRangesOverview.Rnw’ 
   ‘RleTricks.Rnw’ 
** testing if installed package can be loaded

* DONE (IRanges)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.3640.0040.368
DataFrame-class0.5640.0080.569
DataTable-API0.0000.0000.001
DataTable-stats0.0160.0000.014
FilterRules-class0.0400.0000.038
GappedRanges-class0.1920.0000.191
Grouping-class0.2160.0000.216
IRanges-class1.8720.3122.257
IRanges-constructor0.0400.0120.059
IRanges-setops0.1440.0040.159
IRanges-utils1.9000.2922.345
IRangesList-class0.0360.0000.037
IntervalTree-class0.1440.0000.141
List-class0.0040.0000.004
MaskCollection-class0.1560.0000.162
RDApplyParams-class0.6080.0040.631
RangedData-class1.3880.0081.517
RangedData-utils0.0760.0000.082
RangedDataList-class0.0320.0000.033
RangedSelection-class0.0200.0000.021
Ranges-class0.0600.0000.064
Ranges-comparison0.0240.0040.025
Ranges-utils0.1200.0040.127
RangesList-class0.1440.0000.145
RangesList-utils0.3720.0240.400
RangesMatching-class0.0080.0000.007
Rle-class0.1040.0080.125
RleViews-class0.0520.0000.054
RleViewsList-class0.0560.0000.063
SimpleList-class0.0040.0000.006
Vector-class0.0040.0000.005
Views-class0.3040.0000.318
Views-utils0.0480.0000.048
ViewsList-class0.0040.0000.001
XDoubleViews-class0.0520.0000.055
XIntegerViews-class0.0480.0000.047
XVector-class0.0360.0000.038
compact0.4760.0040.478
coverage0.0800.0000.077
disjoin0.0160.0000.016
endoapply0.0080.0000.009
isConstant0.0040.0000.003
nearest0.0280.0040.031
read.Mask0.0360.0040.043
reverse0.0640.0000.065
runstat0.0320.0000.030
seqapply0.0560.0000.055
strutils0.0000.0000.001