BioC 3.4: CHECK report for diffHic on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.5.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/diffHic.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffHic/DESCRIPTION’ ... OK
* this is package ‘diffHic’ version ‘1.5.5’
* 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 ‘diffHic’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.4Mb
* 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 loading without being on the library search path ... 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 ... OK
* 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 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
normalizeCNV 8.48  0.008   8.487
cutGenome    4.94  0.096   5.089
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-basic.R’
  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/diffHic.Rcheck/00check.log’
for details.

* installing *source* package ‘diffHic’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c binner.cpp -o binner.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c check_input.cpp -o check_input.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c cluster_2d.cpp -o cluster_2d.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c count_background.cpp -o count_background.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c count_connect.cpp -o count_connect.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c count_patch.cpp -o count_patch.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c directionality.cpp -o directionality.o
directionality.cpp: In function ‘SEXPREC* directionality(SEXP, SEXP, SEXP, SEXP, SEXP)’:
directionality.cpp:48:9: warning: unused variable ‘current_average’ [-Wunused-variable]
  double current_average;
         ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c iterative_correction.cpp -o iterative_correction.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c nb_average.cpp -o nb_average.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c neighbors.cpp -o neighbors.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c pair_stats.cpp -o pair_stats.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c quadrant_bg.cpp -o quadrant_bg.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c report_hic_pairs.cpp -o report_hic_pairs.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2  -Wall -c trended_filter.cpp -o trended_filter.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o diffHic.so binner.o check_input.o cluster_2d.o count_background.o count_connect.o count_patch.o directionality.o init.o iterative_correction.o nb_average.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o -L/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/diffHic.Rcheck/diffHic/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffHic)

name	user	system	elapsed
DNaseHiC	0.632	0.012	0.645
annotatePairs	0.256	0.004	0.271
boxPairs	0.884	0.012	0.896
clusterPairs	0.500	0.004	0.505
compartmentalize	0.288	0.008	0.294
connectCounts	0.804	0.000	0.806
consolidatePairs	0.268	0.000	0.271
correctedContact	0.224	0.000	0.223
cutGenome	4.940	0.096	5.089
diClusters	1.420	0.000	1.422
diffHicUsersGuide	0.000	0.000	0.001
domainDirections	0.132	0.000	0.130
enrichedPairs	0.052	0.000	0.053
filterDiag	0.136	0.000	0.136
filterPeaks	0.044	0.000	0.044
filters	0.104	0.000	0.103
getArea	0.100	0.004	0.102
getPairData	0.072	0.004	0.075
loadData	0.096	0.000	0.096
marginCounts	0.616	0.004	0.621
mergePairs	0.324	0.012	0.339
neighborCounts	0.468	0.004	0.472
normalizeCNV	8.480	0.008	8.487
pairParam	0.060	0.000	0.062
plotDI	0.348	0.004	0.355
plotPlaid	1.136	0.004	1.204
preparePairs	0.248	0.016	0.266
prunePairs	0.636	0.008	0.653
savePairs	0.112	0.004	0.114
squareCounts	1.252	0.004	1.559
totalCounts	0.888	0.004	1.017

BioC 3.4: CHECK report for diffHic on zin1

Summary

Command output