IRanges 2.4.1
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/IRanges | | Last Changed Rev: 109784 / Revision: 109947 | | Last Changed Date: 2015-10-20 02:25:43 -0400 (Tue, 20 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ OK ] | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL IRanges
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.2-bioc/R/library’
* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c NCList.c -o NCList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c Ranges_class.c -o Ranges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -fpic -g -O2 -Wall -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;
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/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:168:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
delta += gapwidth;
^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/R/library/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Hits","PartitioningByEnd"’: no definition for class “PartitioningByEnd”
in method for ‘coerce’ with signature ‘"Hits","Partitioning"’: no definition for class “Partitioning”
in method for ‘coerce’ with signature ‘"Hits","Ranges"’: no definition for class “Ranges”
in method for ‘coerce’ with signature ‘"Hits","IRanges"’: no definition for class “IRanges”
in method for ‘coerce’ with signature ‘"Hits","CompressedIntegerList"’: no definition for class “CompressedIntegerList”
in method for ‘coerce’ with signature ‘"Hits","IntegerList"’: no definition for class “IntegerList”
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
in method for ‘!’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","list"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","vector"’: no definition for class “CompressedList”
in method for ‘duplicated’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘unique’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘is.na’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
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 ‘split<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ 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 ‘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 ‘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
* DONE (IRanges)