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BioC 3.0: CHECK report for DiffBind on zin1

This page was generated on 2015-04-10 09:39:34 -0700 (Fri, 10 Apr 2015).

Package 242/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffBind 1.12.3
Rory Stark
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DiffBind
Last Changed Rev: 100530 / Revision: 102249
Last Changed Date: 2015-03-11 06:01:17 -0700 (Wed, 11 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]
moscato1 Windows Server 2008 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 

Summary

Package: DiffBind
Version: 1.12.3
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DiffBind_1.12.3.tar.gz
StartedAt: 2015-04-09 23:20:28 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:26:15 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 347.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: DiffBind.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DiffBind_1.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/DiffBind.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.3’
* 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 ... [23s/24s] 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
'library' or 'require' calls in package code:
  ‘BiocParallel’ ‘DESeq’ ‘DESeq2’ ‘Rsamtools’ ‘parallel’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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.biocparallel.lapply: no visible global function definition for
  ‘bplapply’
dba.lsfR.init: no visible global function definition for
  ‘dba.CRI.lsfR.init’
dba.multicore.addjob: no visible global function definition for
  ‘mcparallel’
dba.multicore.lapply: no visible global function definition for
  ‘mclapply’
dba.multicore.wait4jobs: no visible global function definition for
  ‘mccollect’
pv.DEinit: no visible global function definition for ‘newCountDataSet’
pv.getCountsLowMem: no visible global function definition for
  ‘BamFileList’
pv.getCountsLowMem: no visible global function definition for
  ‘ScanBamParam’
pv.getCountsLowMem: no visible global function definition for
  ‘scanBamFlag’
pv.getCountsLowMem: no visible global function definition for
  ‘countBam’
* 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 GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [155s/155s] 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/DiffBind.Rcheck/00check.log’
for details.

DiffBind.Rcheck/00install.out:

* installing *source* package ‘DiffBind’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c bedReader.cpp -o bedReader.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c bitBucket.cpp -o bitBucket.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c croi_func.cpp -o croi_func.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c croi_main.cpp -o croi_main.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c densitySet.cpp -o densitySet.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c iBucket.cpp -o iBucket.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c interval.cpp -o interval.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c intervalDensity.cpp -o intervalDensity.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c intervalNode.cpp -o intervalNode.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c intervalSet.cpp -o intervalSet.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c intervalTree.cpp -o intervalTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c nodeGroup.cpp -o nodeGroup.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c reader.cpp -o reader.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c sequence.cpp -o sequence.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c util.cpp -o util.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o DiffBind.so bamReader.o bedReader.o bitBucket.o croi_func.o croi_main.o densitySet.o iBucket.o interval.o intervalDensity.o intervalNode.o intervalSet.o intervalTree.o mergeOne.o nodeGroup.o reader.o sequence.o util.o /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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)

DiffBind.Rcheck/DiffBind-Ex.timings:

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