BioC 3.1: CHECK report for diffHic on zin2

Package: diffHic

Version: 1.0.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.0.1.tar.gz

StartedAt: 2015-10-09 00:33:39 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:39:08 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 329.0 seconds

RetCode: 0

Status:  OK

CheckDir: diffHic.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.0.1’
* 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 ... [26s/41s] 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 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 ... [30s/46s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
normalizeCNV 8.821  0.000  14.174
cutGenome    4.938  0.042   7.432
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-basic.R’ [9s/13s]
  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ...6d5
< Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
 [9s/13s] 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: OK

* installing *source* package ‘diffHic’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c count_marginals.cpp -o count_marginals.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-bioc/R/lib -L/usr/local/lib -o diffHic.so check_input.o cluster_2d.o count_connect.o count_marginals.o count_patch.o init.o iterative_correction.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/diffHic.Rcheck/diffHic/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (diffHic)

name	user	system	elapsed
DIList	0.156	0.004	0.199
DNaseHiC	1.036	0.020	1.699
boxPairs	0.387	0.031	0.595
clusterPairs	0.300	0.001	0.465
connectCounts	0.967	0.000	1.283
consolidatePairs	0.422	0.004	0.505
correctedContact	0.075	0.000	0.143
cutGenome	4.938	0.042	7.432
diffHicUsersGuide	0.002	0.000	0.014
enrichedPairs	0.156	0.000	0.196
filterPeaks	0.052	0.000	0.053
filters	0.033	0.000	0.036
getArea	0.116	0.004	0.243
getDistance	0.016	0.000	0.019
getPairData	0.067	0.000	0.067
loadData	0.075	0.000	0.075
marginCounts	0.680	0.004	0.849
mergePairs	0.175	0.016	0.327
normalizeCNV	8.821	0.000	14.174
pairParam	0.062	0.000	0.117
plotDI	0.464	0.004	0.860
plotPlaid	1.241	0.004	1.717
preparePairs	0.162	0.000	0.164
prunePairs	0.201	0.008	0.361
savePairs	0.051	0.000	0.103
squareCounts	0.994	0.004	1.720
totalCounts	0.635	0.004	1.279