IRanges 1.20.7
Bioconductor Package Maintainer
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/IRanges | | Last Changed Rev: 87131 / Revision: 88450 | | Last Changed Date: 2014-03-05 13:40:53 -0800 (Wed, 05 Mar 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/IRanges.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.20.7’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘IRanges’ can be installed ... [22s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘utils’ ‘stats’ ‘BiocGenerics’
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
* 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:
‘stats:::na.exclude.data.frame’ ‘stats:::na.omit.data.frame’
‘stats:::window.default’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... WARNING
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 ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘levels.OverlapEncodings’ ‘splitAsList’ ‘splitAsListReturnedClass’
‘subsetByRanges’
Undocumented S4 methods:
generic 'splitAsListReturnedClass' and siglist 'ANY'
generic 'splitAsListReturnedClass' and siglist 'DataFrame'
generic 'splitAsListReturnedClass' and siglist 'Hits'
generic 'splitAsListReturnedClass' and siglist 'data.frame'
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 ... OK
* 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 ... WARNING
File ‘/home/biocbuild/bbs-2.13-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 entry points 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘IRangesOverview.Rnw’, ‘RleTricks.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [13s/13s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘IRanges_unit_tests.R’ [42s/42s]
[42s/42s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 3 warnings.
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/IRanges.Rcheck/00check.log’
for details.
* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Hits_class.c -o Hits_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap_first’:
IntervalTree.c:500:20: warning: variable ‘nhits’ set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap_last’:
IntervalTree.c:574:20: warning: variable ‘nhits’ set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function ‘_IntegerIntervalTree_overlap’:
IntervalTree.c:365:3: warning: ‘result_inds’ may be used uninitialized in this function [-Wuninitialized]
IntervalTree.c: In function ‘_IntegerIntervalForest_overlap’:
IntervalTree.c:393:17: warning: ‘result_inds’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rle_class.c -o Rle_class.o
Rle_class.c: In function ‘compute_CHARSXP_runs’:
Rle_class.c:132:31: warning: ‘val0’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rle_utils.c -o Rle_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Vector_class.c -o Vector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘cachedIRanges_coverage’:
coverage_methods.c:501:37: warning: ‘x_end’ may be used uninitialized in this function [-Wuninitialized]
coverage_methods.c:417:21: note: ‘x_end’ was declared here
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash_utils.c -o hash_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c int_utils.c -o int_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function ‘reduce_ranges’:
inter_range_methods.c:177:21: warning: ‘mapping_elt’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:183:35: warning: ‘delta’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:166:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:168:14: warning: ‘max_end’ may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:143:6: warning: ‘append_or_drop’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c memalloc.c -o memalloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c safe_arithm.c -o safe_arithm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ucsc_handlers.c -o ucsc_handlers.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 IntervalTree.o R_init_IRanges.o RangedData_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o encodeOverlaps_methods.o errabort.o hash_utils.o int_utils.o inter_range_methods.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
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 ‘window’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘subset’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Vector","double"’: no definition for class “double”
Creating a generic function for ‘relist’ from package ‘utils’ in package ‘IRanges’
in method for ‘relist’ with signature ‘"ANY","PartitioningByEnd"’: no definition for class “PartitioningByEnd”
in method for ‘relist’ with signature ‘"ANY","List"’: no definition for class “List”
Creating a generic function for ‘split’ 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 ‘%in%’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘as.list’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘unsplit’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘stack’ from package ‘utils’ 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 ‘as.matrix’ 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 ‘by’ 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.factor’ 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’
in method for ‘coerce’ with signature ‘"xtabs","DataFrame"’: no definition for class “xtabs”
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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)