BioC 3.2: CHECK report for diffHic on zin1

Package: diffHic

Version: 1.2.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.2.2.tar.gz

StartedAt: 2016-04-23 00:04:19 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:08:22 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 243.5 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_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/diffHic.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.2.2’
* 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 ... [34s/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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/32s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
normalizeCNV 9.387  0.004   9.425
cutGenome    5.264  0.013   5.336
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-basic.R’ [10s/10s]
  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
 [10s/10s] 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	0.143	0.000	0.143
DNaseHiC	0.766	0.028	0.805
boxPairs	0.648	0.000	0.649
clusterPairs	0.288	0.004	0.293
compartmentalize	0.173	0.000	0.174
connectCounts	0.812	0.008	0.827
consolidatePairs	0.313	0.000	0.312
correctedContact	0.205	0.004	0.210
cutGenome	5.264	0.013	5.336
diffHicUsersGuide	0.002	0.000	0.001
domainDirections	0.249	0.020	0.269
enrichedPairs	0.036	0.000	0.036
filterDiag	0.153	0.000	0.153
filterPeaks	0.028	0.000	0.029
filters	0.076	0.000	0.076
getArea	0.103	0.000	0.104
getDistance	0.02	0.00	0.02
getPairData	0.07	0.00	0.07
loadData	0.079	0.000	0.079
marginCounts	0.642	0.004	0.645
mergePairs	0.175	0.008	0.183
neighborCounts	0.246	0.004	0.250
normalizeCNV	9.387	0.004	9.425
pairParam	0.068	0.000	0.068
plotDI	0.41	0.00	0.41
plotPlaid	1.149	0.003	1.155
preparePairs	0.165	0.004	0.169
prunePairs	0.216	0.000	0.217
savePairs	0.05	0.00	0.05
squareCounts	0.801	0.000	0.802
totalCounts	0.530	0.004	0.534
wrappers	0.036	0.000	0.036