BioC 3.5: CHECK report for diffHic on veracruz2

Package: diffHic

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.8.1.tar.gz

StartedAt: 2017-08-16 02:01:33 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:07:18 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 345.2 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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/diffHic.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffHic/DESCRIPTION’ ... OK
* this is package ‘diffHic’ version ‘1.8.1’
* 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 ... 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 9.745  0.068   10.09
* 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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c binner.cpp -o binner.o
binner.cpp:36:84: warning: field 'ischanged' will be initialized after field 'curcounts' [-Wreorder]
binner::binner(SEXP all, SEXP bin, int f, int l) : fbin(f), lbin(l), nbins(l-f+1), ischanged(NULL), curcounts(NULL) {
                                                                                   ^
In file included from binner.cpp:1:
./read_count.h:42:36: warning: private field 'lib' is not used [-Wunused-private-field]
        int curab, curtb, curlib, curdex, lib;
                                          ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c check_input.cpp -o check_input.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cluster_2d.cpp -o cluster_2d.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_background.cpp -o count_background.o
count_background.cpp:249:10: warning: unused variable 'backaverage' [-Wunused-variable]
                double backaverage, maxaverage;
                       ^
count_background.cpp:249:23: warning: unused variable 'maxaverage' [-Wunused-variable]
                double backaverage, maxaverage;
                                    ^
2 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_connect.cpp -o count_connect.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_patch.cpp -o count_patch.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c directionality.cpp -o directionality.o
directionality.cpp:45:9: warning: unused variable 'current_average' [-Wunused-variable]
        double current_average;
               ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c iterative_correction.cpp -o iterative_correction.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c neighbors.cpp -o neighbors.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pair_stats.cpp -o pair_stats.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c quadrant_bg.cpp -o quadrant_bg.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c report_hic_pairs.cpp -o report_hic_pairs.o
report_hic_pairs.cpp:575:6: warning: private field 'bin_width' is not used [-Wunused-private-field]
        int bin_width;
            ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -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 neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/lib/libhts.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.5-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	0.593	0.009	0.620
annotatePairs	1.502	0.039	1.614
boxPairs	1.287	0.009	1.350
clusterPairs	0.863	0.006	0.901
compartmentalize	0.828	0.019	0.874
connectCounts	1.349	0.013	1.410
consolidatePairs	0.471	0.002	0.484
correctedContact	0.298	0.005	0.310
cutGenome	4.321	0.090	4.557
diClusters	1.293	0.008	1.337
diffHicUsersGuide	0.001	0.000	0.002
domainDirections	0.241	0.005	0.258
enrichedPairs	0.224	0.001	0.228
filterDiag	0.149	0.004	0.157
filterPeaks	0.237	0.001	0.244
filters	0.128	0.000	0.139
getArea	0.173	0.002	0.178
getPairData	0.064	0.004	0.068
loadData	0.083	0.005	0.088
marginCounts	0.662	0.007	0.690
mergePairs	0.329	0.012	0.343
neighborCounts	0.170	0.003	0.179
normalizeCNV	9.745	0.068	10.090
pairParam	0.109	0.002	0.112
plotDI	1.127	0.011	1.172
plotPlaid	1.260	0.013	1.301
preparePairs	0.438	0.024	0.473
prunePairs	0.525	0.015	0.571
savePairs	0.081	0.003	0.085
squareCounts	0.939	0.011	0.962
totalCounts	0.713	0.009	0.742