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: 2017-10-18 02:46:47 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:52:43 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 355.8 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 3.4.2 (2017-09-28)
* 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 8.799  0.084   9.082
* 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	0.679	0.010	0.707
annotatePairs	1.453	0.050	1.547
boxPairs	1.352	0.013	1.406
clusterPairs	0.843	0.009	0.868
compartmentalize	0.964	0.020	1.008
connectCounts	1.413	0.016	1.463
consolidatePairs	0.450	0.004	0.460
correctedContact	0.305	0.007	0.324
cutGenome	4.376	0.105	4.638
diClusters	0.827	0.006	0.863
diffHicUsersGuide	0.001	0.000	0.001
domainDirections	0.240	0.006	0.289
enrichedPairs	0.178	0.001	0.180
filterDiag	0.122	0.003	0.128
filterPeaks	0.173	0.001	0.178
filters	0.101	0.001	0.106
getArea	0.145	0.003	0.151
getPairData	0.047	0.003	0.052
loadData	0.063	0.005	0.071
marginCounts	0.632	0.011	0.656
mergePairs	0.292	0.014	0.311
neighborCounts	0.148	0.005	0.156
normalizeCNV	8.799	0.084	9.082
pairParam	0.092	0.002	0.095
plotDI	1.101	0.014	1.152
plotPlaid	1.079	0.016	1.141
preparePairs	0.391	0.024	0.432
prunePairs	0.509	0.017	0.542
savePairs	0.096	0.003	0.100
squareCounts	1.032	0.013	1.090
totalCounts	0.763	0.013	0.809