BioC 3.6: CHECK report for IRanges on tokay1
This page was generated on 2017-08-16 13:26:21 -0400 (Wed, 16 Aug 2017).
IRanges 2.11.12
Bioconductor Package Maintainer
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges | | Last Changed Rev: 131496 / Revision: 131943 | | Last Changed Date: 2017-07-21 17:13:59 -0400 (Fri, 21 Jul 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
| Package: IRanges
|
| Version: 2.11.12
|
| Command: rm -rf IRanges.buildbin-libdir IRanges.Rcheck && mkdir IRanges.buildbin-libdir IRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IRanges.buildbin-libdir IRanges_2.11.12.tar.gz >IRanges.Rcheck\00install.out 2>&1 && cp IRanges.Rcheck\00install.out IRanges-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IRanges.buildbin-libdir --install="check:IRanges-install.out" --force-multiarch --no-vignettes --timings IRanges_2.11.12.tar.gz
|
| StartedAt: 2017-08-16 00:20:54 -0400 (Wed, 16 Aug 2017)
|
| EndedAt: 2017-08-16 00:26:49 -0400 (Wed, 16 Aug 2017)
|
| EllapsedTime: 354.7 seconds
|
| RetCode: 0
|
| Status: WARNINGS
|
| CheckDir: IRanges.Rcheck
|
| Warnings: 2
|
Command output
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###
### Running command:
###
### rm -rf IRanges.buildbin-libdir IRanges.Rcheck && mkdir IRanges.buildbin-libdir IRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IRanges.buildbin-libdir IRanges_2.11.12.tar.gz >IRanges.Rcheck\00install.out 2>&1 && cp IRanges.Rcheck\00install.out IRanges-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IRanges.buildbin-libdir --install="check:IRanges-install.out" --force-multiarch --no-vignettes --timings IRanges_2.11.12.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '2.11.12'
* 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 'IRanges' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setCompressedListSummaryMethod : <anonymous>: no visible binding for
global variable 'C_fun'
setCompressedListWhichSummaryMethod : def: no visible binding for
global variable 'C_fun'
Undefined global functions or variables:
C_fun
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'%poutside%' '%pover%' '%pwithin%' 'slidingIRanges' 'slidingViews'
Undocumented S4 methods:
generic 'anyDuplicated' and siglist 'RangesNSBS'
generic 'as.factor' and siglist 'ManyToOneGrouping'
generic 'c' and siglist 'SimpleList'
generic 'cbind' and siglist 'Rle'
generic 'cbind' and siglist 'RleList'
generic 'coerce' and siglist 'AtomicList,RleViews'
generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
generic 'coerce' and siglist 'factor,ManyToOneGrouping'
generic 'colnames' and siglist 'SDFLWrapperForTransform'
generic 'colnames' and siglist 'SplitDataFrameList'
generic 'ifelse2' and siglist 'ANY,List,List'
generic 'is.unsorted' and siglist 'CompressedIntegerList'
generic 'is.unsorted' and siglist 'CompressedLogicalList'
generic 'is.unsorted' and siglist 'CompressedNumericList'
generic 'length' and siglist 'RangesNSBS'
generic 'pcompareRecursively' and siglist 'Ranges'
generic 'relist' and siglist 'grouping,missing'
generic 'showAsCell' and siglist 'Views'
generic 'splitAsList' and siglist 'ANY'
generic 'stack' and siglist 'matrix'
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 ... WARNING
Documented arguments not in \usage in documentation object 'nearest-methods':
'hits'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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-3.6-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386/IRanges.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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
IPos-class 7.91 0.3 8.2
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
IPos-class 9.56 0.2 9.77
* 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 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
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.Rcheck/00check.log'
for details.
IRanges.Rcheck/00install.out:
install for i386
* installing *source* package 'IRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
static const NCList *next_top_down(const NCList *nclist)
^
NCList.c:1163:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
^
NCList.c: In function 'NCList_find_overlaps':
NCList.c:1452:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans;
^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1532:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*out_ranges_are_tiles && x_end != cvg_len)
^
coverage_methods.c:419:21: note: 'x_end' was declared here
i, j, x_start, x_end, shift_elt, tmp;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'Ranges_reduce':
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
delta += gapwidth;
^
inter_range_methods.c:102:31: note: 'gapwidth' was declared here
append_or_drop, max_end, gapwidth, delta, width_inc;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'drop' from package 'base' 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 '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'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'IRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
static const NCList *next_top_down(const NCList *nclist)
^
NCList.c:1163:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1532:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*out_ranges_are_tiles && x_end != cvg_len)
^
coverage_methods.c:419:21: note: 'x_end' was declared here
i, j, x_start, x_end, shift_elt, tmp;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:165:5: warning: 'revmap_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(revmap_elt,
^
inter_range_methods.c:154:11: warning: 'delta' may be used uninitialized in this function [-Wmaybe-uninitialized]
delta += gapwidth;
^
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
inter_range_methods.c:156:14: warning: 'max_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
width_inc = end_j - max_end;
^
inter_range_methods.c:131:6: warning: 'append_or_drop' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (append_or_drop) {
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.11.12.zip
* DONE (IRanges)
IRanges.Rcheck/examples_i386/IRanges-Ex.timings:
| name | user | system | elapsed
|
| AtomicList-class | 0.39 | 0.00 | 0.39 |
|
| AtomicList-utils | 0.05 | 0.00 | 0.04 |
|
| CompressedList-class | 0 | 0 | 0 |
|
| DataFrame-utils | 0.22 | 0.00 | 0.22 |
|
| Grouping-class | 0.09 | 0.00 | 0.09 |
|
| Hits-class-leftovers | 0.2 | 0.0 | 0.2 |
|
| IPos-class | 7.91 | 0.30 | 8.20 |
|
| IRanges-class | 2.15 | 0.03 | 2.19 |
|
| IRanges-constructor | 0.07 | 0.00 | 0.06 |
|
| IRanges-utils | 1.83 | 0.03 | 1.86 |
|
| IRangesList-class | 0.04 | 0.00 | 0.05 |
|
| List-class-leftovers | 0 | 0 | 0 |
|
| MaskCollection-class | 0.09 | 0.03 | 0.12 |
|
| NCList-class | 0.06 | 0.00 | 0.06 |
|
| RangedData-class | 1.10 | 0.03 | 1.13 |
|
| RangedSelection-class | 0.03 | 0.00 | 0.03 |
|
| Ranges-class | 0.06 | 0.00 | 0.06 |
|
| Ranges-comparison | 0.06 | 0.00 | 0.07 |
|
| RangesList-class | 0.04 | 0.00 | 0.03 |
|
| Rle-class-leftovers | 0 | 0 | 0 |
|
| RleViews-class | 0.07 | 0.00 | 0.07 |
|
| RleViewsList-class | 0.07 | 0.00 | 0.07 |
|
| Views-class | 0.06 | 0.00 | 0.06 |
|
| ViewsList-class | 0 | 0 | 0 |
|
| bind-arrays | 0.01 | 0.00 | 0.02 |
|
| coverage-methods | 0.18 | 0.00 | 0.17 |
|
| extractList | 0.04 | 0.00 | 0.04 |
|
| findOverlaps-methods | 0.27 | 0.00 | 0.27 |
|
| inter-range-methods | 0.83 | 0.00 | 0.83 |
|
| intra-range-methods | 0.22 | 0.00 | 0.22 |
|
| multisplit | 0.01 | 0.00 | 0.01 |
|
| nearest-methods | 0.08 | 0.00 | 0.08 |
|
| range-squeezers | 0 | 0 | 0 |
|
| read.Mask | 0.08 | 0.00 | 0.08 |
|
| reverse-methods | 0.06 | 0.00 | 0.06 |
|
| setops-methods | 0.16 | 0.00 | 0.16 |
|
| slice-methods | 0.01 | 0.00 | 0.01 |
|
| view-summarization-methods | 0.02 | 0.00 | 0.02 |
|
IRanges.Rcheck/examples_x64/IRanges-Ex.timings:
| name | user | system | elapsed
|
| AtomicList-class | 0.46 | 0.00 | 0.47 |
|
| AtomicList-utils | 0.05 | 0.00 | 0.04 |
|
| CompressedList-class | 0 | 0 | 0 |
|
| DataFrame-utils | 0.27 | 0.00 | 0.27 |
|
| Grouping-class | 0.09 | 0.00 | 0.09 |
|
| Hits-class-leftovers | 0.14 | 0.00 | 0.14 |
|
| IPos-class | 9.56 | 0.20 | 9.77 |
|
| IRanges-class | 3.13 | 0.06 | 3.19 |
|
| IRanges-constructor | 0.06 | 0.00 | 0.06 |
|
| IRanges-utils | 2.69 | 0.03 | 2.72 |
|
| IRangesList-class | 0.05 | 0.00 | 0.04 |
|
| List-class-leftovers | 0.01 | 0.00 | 0.02 |
|
| MaskCollection-class | 0.13 | 0.00 | 0.12 |
|
| NCList-class | 0.04 | 0.01 | 0.06 |
|
| RangedData-class | 1.36 | 0.04 | 1.39 |
|
| RangedSelection-class | 0.05 | 0.00 | 0.05 |
|
| Ranges-class | 0.06 | 0.00 | 0.06 |
|
| Ranges-comparison | 0.07 | 0.01 | 0.08 |
|
| RangesList-class | 0.03 | 0.00 | 0.03 |
|
| Rle-class-leftovers | 0.01 | 0.00 | 0.02 |
|
| RleViews-class | 0.06 | 0.00 | 0.06 |
|
| RleViewsList-class | 0.10 | 0.00 | 0.09 |
|
| Views-class | 0.09 | 0.00 | 0.10 |
|
| ViewsList-class | 0 | 0 | 0 |
|
| bind-arrays | 0 | 0 | 0 |
|
| coverage-methods | 0.21 | 0.00 | 0.20 |
|
| extractList | 0.06 | 0.00 | 0.06 |
|
| findOverlaps-methods | 0.34 | 0.00 | 0.35 |
|
| inter-range-methods | 0.61 | 0.00 | 0.61 |
|
| intra-range-methods | 0.26 | 0.00 | 0.27 |
|
| multisplit | 0.03 | 0.00 | 0.03 |
|
| nearest-methods | 0.11 | 0.00 | 0.11 |
|
| range-squeezers | 0 | 0 | 0 |
|
| read.Mask | 0.08 | 0.00 | 0.08 |
|
| reverse-methods | 0.08 | 0.00 | 0.08 |
|
| setops-methods | 0.2 | 0.0 | 0.2 |
|
| slice-methods | 0 | 0 | 0 |
|
| view-summarization-methods | 0.03 | 0.00 | 0.03 |
|