DiffBind 1.8.5
Rory Stark
| 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/DiffBind | | Last Changed Rev: 88368 / Revision: 88450 | | Last Changed Date: 2014-04-03 05:44:29 -0700 (Thu, 03 Apr 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/DiffBind.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 ‘DiffBind/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffBind’ version ‘1.8.5’
* 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 ‘DiffBind’ can be installed ... [14s/14s] 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
* 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
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘DBA_DATA_GRANGES’ ‘overLapper’ ‘pv.listadd’ ‘vennPlot’
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 ... NOTE
dba.Rlsf.init: no visible global function definition for
‘dba.CRI.Rlsf.init’
dba.lsfR.init: no visible global function definition for
‘dba.CRI.lsfR.init’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘DiffBind.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [100s/99s] 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/DiffBind.Rcheck/00check.log’
for details.
* installing *source* package ‘DiffBind’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c bamReader.cpp -o bamReader.o
bamReader.cpp: In member function ‘bool bode::BamReader::isBam(const string&)’:
bamReader.cpp:14:7: warning: variable ‘rd’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c bedReader.cpp -o bedReader.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c bitBucket.cpp -o bitBucket.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c croi_func.cpp -o croi_func.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c croi_main.cpp -o croi_main.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c iBucket.cpp -o iBucket.o
iBucket.cpp: In member function ‘int IBucket::bsearch(int, int, int)’:
iBucket.cpp:69:3: warning: ‘mid’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c interval.cpp -o interval.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c intervalNode.cpp -o intervalNode.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c intervalSet.cpp -o intervalSet.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c intervalTree.cpp -o intervalTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c mergeOne.c -o mergeOne.o
mergeOne.c: In function ‘mo_mergeTwo’:
mergeOne.c:351:7: warning: variable ‘keepAll’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c nodeGroup.cpp -o nodeGroup.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c reader.cpp -o reader.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c sequence.cpp -o sequence.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c util.cpp -o util.o
g++ -shared -L/usr/local/lib -o DiffBind.so bamReader.o bedReader.o bitBucket.o croi_func.o croi_main.o iBucket.o interval.o intervalNode.o intervalSet.o intervalTree.o mergeOne.o nodeGroup.o reader.o sequence.o util.o /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/DiffBind.Rcheck/DiffBind/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DiffBind)