BioC 3.4: CHECK report for diffHic on morelia

Package: diffHic

Version: 1.5.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.5.5.tar.gz

StartedAt: 2016-09-20 05:38:18 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:42:48 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 270.5 seconds

RetCode: 0

Status:  OK

CheckDir: diffHic.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.5.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/diffHic.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ... 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 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 10.846  0.090  10.971
cutGenome     6.751  0.182   7.641
* 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: OK

* installing *source* package ‘diffHic’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c binner.cpp -o binner.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c check_input.cpp -o check_input.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cluster_2d.cpp -o cluster_2d.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c count_background.cpp -o count_background.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c count_connect.cpp -o count_connect.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c count_patch.cpp -o count_patch.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c directionality.cpp -o directionality.o
directionality.cpp:48:9: warning: unused variable 'current_average' [-Wunused-variable]
        double current_average;
               ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c iterative_correction.cpp -o iterative_correction.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c nb_average.cpp -o nb_average.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c neighbors.cpp -o neighbors.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pair_stats.cpp -o pair_stats.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c quadrant_bg.cpp -o quadrant_bg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c report_hic_pairs.cpp -o report_hic_pairs.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c trended_filter.cpp -o trended_filter.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/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	1.171	0.035	1.481
annotatePairs	0.352	0.014	0.367
boxPairs	1.036	0.027	1.065
clusterPairs	0.698	0.004	0.704
compartmentalize	0.336	0.007	0.344
connectCounts	0.971	0.011	1.012
consolidatePairs	0.260	0.001	0.261
correctedContact	0.177	0.006	0.183
cutGenome	6.751	0.182	7.641
diClusters	2.178	0.022	2.218
diffHicUsersGuide	0.002	0.000	0.002
domainDirections	0.269	0.009	0.278
enrichedPairs	0.109	0.001	0.110
filterDiag	0.256	0.007	0.265
filterPeaks	0.082	0.001	0.083
filters	0.207	0.002	0.210
getArea	0.181	0.003	0.184
getPairData	0.144	0.007	0.154
loadData	0.167	0.008	0.176
marginCounts	1.193	0.014	1.297
mergePairs	0.395	0.015	0.420
neighborCounts	0.703	0.008	0.785
normalizeCNV	10.846	0.090	10.971
pairParam	0.134	0.002	0.136
plotDI	0.805	0.007	0.816
plotPlaid	2.040	0.020	2.079
preparePairs	0.343	0.019	0.364
prunePairs	0.685	0.020	0.706
savePairs	0.083	0.003	0.086
squareCounts	1.019	0.011	1.030
totalCounts	1.051	0.012	1.065