BioC 3.6: CHECK report for diffHic on malbec1

Package: diffHic

Version: 1.9.4

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.9.4.tar.gz

StartedAt: 2017-08-15 22:38:14 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:42:51 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 277.2 seconds

RetCode: 0

Status:  OK

CheckDir: diffHic.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.9.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/diffHic.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.9.4’
* 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 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 7.948  0.000   7.954
cutGenome    4.672  0.136   5.293
* 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
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c binner.cpp -o binner.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c check_input.cpp -o check_input.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c cluster_2d.cpp -o cluster_2d.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c count_background.cpp -o count_background.o
count_background.cpp: In function ‘SEXPREC* count_background(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
count_background.cpp:253:10: warning: unused variable ‘backaverage’ [-Wunused-variable]
   double backaverage, maxaverage;
          ^
count_background.cpp:253:23: warning: unused variable ‘maxaverage’ [-Wunused-variable]
   double backaverage, maxaverage;
                       ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c count_connect.cpp -o count_connect.o
count_connect.cpp: In function ‘SEXPREC* count_reconnect(SEXP, SEXP)’:
count_connect.cpp:299:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (size_t odex=0; odex < ncombos; ++odex) { 
                            ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c count_patch.cpp -o count_patch.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c directionality.cpp -o directionality.o
directionality.cpp: In function ‘SEXPREC* directionality(SEXP, SEXP, SEXP, SEXP, SEXP)’:
directionality.cpp:43:9: warning: unused variable ‘vecdex’ [-Wunused-variable]
  size_t vecdex;
         ^
directionality.cpp:45:9: warning: unused variable ‘current_average’ [-Wunused-variable]
  double current_average;
         ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c iterative_correction.cpp -o iterative_correction.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c neighbors.cpp -o neighbors.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pair_stats.cpp -o pair_stats.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c quadrant_bg.cpp -o quadrant_bg.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c report_hic_pairs.cpp -o report_hic_pairs.o
report_hic_pairs.cpp: In constructor ‘segment::segment()’:
report_hic_pairs.cpp:14:9: warning: ‘segment::fragid’ will be initialized after [-Wreorder]
     int fragid;
         ^
report_hic_pairs.cpp:13:27: warning:   ‘const int segment::chrid’ [-Wreorder]
  const int offset, width, chrid, pos;
                           ^
report_hic_pairs.cpp:11:5: warning:   when initialized here [-Wreorder]
     segment() : offset(0), width(0), fragid(NA_INTEGER), chrid(0), pos(0), reverse(false) {}
     ^
report_hic_pairs.cpp: In constructor ‘segment::segment(int, int, bool, int, int)’:
report_hic_pairs.cpp:15:13: warning: ‘segment::reverse’ will be initialized after [-Wreorder]
  const bool reverse;
             ^
report_hic_pairs.cpp:13:12: warning:   ‘const int segment::offset’ [-Wreorder]
  const int offset, width, chrid, pos;
            ^
report_hic_pairs.cpp:12:5: warning:   when initialized here [-Wreorder]
     segment(int c, int p, bool r, int o, int w) : chrid(c), pos(p), reverse(r), offset(o), width(w), fragid(NA_INTEGER) {}
     ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c trended_filter.cpp -o trended_filter.o
g++ -shared -L/home/biocbuild/bbs-3.6-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 neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o -L/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.468	0.000	0.502
annotatePairs	1.196	0.008	1.205
boxPairs	1.128	0.004	1.130
clusterPairs	0.624	0.004	0.629
compartmentalize	0.748	0.016	0.764
connectCounts	1.108	0.000	1.108
consolidatePairs	0.508	0.000	0.509
correctedContact	0.324	0.004	0.327
cutGenome	4.672	0.136	5.293
diClusters	0.596	0.000	0.597
diffHicUsersGuide	0.000	0.000	0.001
domainDirections	0.176	0.000	0.179
enrichedPairs	0.192	0.000	0.192
extractPatch	0.564	0.000	0.565
filterDiag	0.100	0.000	0.099
filterPeaks	0.152	0.000	0.152
filters	0.096	0.000	0.096
getArea	0.132	0.000	0.132
getPairData	0.044	0.000	0.043
loadData	0.048	0.000	0.049
marginCounts	0.496	0.000	0.498
mergePairs	0.172	0.008	0.194
neighborCounts	0.160	0.000	0.163
normalizeCNV	7.948	0.000	7.954
pairParam	0.080	0.000	0.079
plotDI	0.472	0.004	0.477
plotPlaid	1.184	0.004	1.188
preparePairs	0.184	0.000	0.184
prunePairs	0.160	0.000	0.157
savePairs	0.044	0.000	0.045
squareCounts	0.676	0.000	0.681
totalCounts	0.400	0.004	0.406