BioC 3.2: CHECK report for diffHic on linux1.bioconductor.org

Package: diffHic

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.2.0.tar.gz

StartedAt: 2015-10-27 02:57:38 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:02:03 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 265.0 seconds

RetCode: 0

Status:  OK

CheckDir: diffHic.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/diffHic.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [35s/35s] 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
normalizeCNV 12.010  0.000  12.034
cutGenome     6.192  0.056   6.262
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-basic.R’ [11s/11s]
  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
 [11s/11s] 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-3.2-bioc/meat/diffHic.Rcheck/00check.log’
for details.

* installing *source* package ‘diffHic’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c binner.cpp -o binner.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c check_input.cpp -o check_input.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cluster_2d.cpp -o cluster_2d.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c count_background.cpp -o count_background.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c count_connect.cpp -o count_connect.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c count_patch.cpp -o count_patch.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c directionality.cpp -o directionality.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c iterative_correction.cpp -o iterative_correction.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nb_average.cpp -o nb_average.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c neighbors.cpp -o neighbors.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pair_stats.cpp -o pair_stats.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c quadrant_bg.cpp -o quadrant_bg.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c report_hic_pairs.cpp -o report_hic_pairs.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c trended_filter.cpp -o trended_filter.o
g++ -shared -L/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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
DIList	0.538	0.004	0.542
DNaseHiC	1.003	0.024	1.033
boxPairs	0.942	0.000	0.943
clusterPairs	0.439	0.004	0.445
compartmentalize	0.194	0.000	0.194
connectCounts	0.760	0.000	0.761
consolidatePairs	0.287	0.000	0.287
correctedContact	0.18	0.00	0.18
cutGenome	6.192	0.056	6.262
diffHicUsersGuide	0.001	0.000	0.001
domainDirections	0.258	0.012	0.270
enrichedPairs	0.029	0.000	0.030
filterDiag	0.130	0.004	0.134
filterPeaks	0.022	0.000	0.021
filters	0.065	0.000	0.066
getArea	0.101	0.000	0.100
getDistance	0.007	0.008	0.015
getPairData	0.060	0.000	0.059
loadData	0.061	0.004	0.065
marginCounts	0.812	0.000	0.812
mergePairs	0.242	0.000	0.243
neighborCounts	0.361	0.004	0.365
normalizeCNV	12.010	0.000	12.034
pairParam	0.097	0.000	0.099
plotDI	0.670	0.000	0.672
plotPlaid	1.714	0.000	1.714
preparePairs	0.203	0.000	0.204
prunePairs	0.266	0.008	0.276
savePairs	0.064	0.000	0.064
squareCounts	1.246	0.004	1.250
totalCounts	0.536	0.000	0.537
wrappers	0.029	0.000	0.029