BioC 3.1: CHECK report for diffHic on petty

Package: diffHic

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.0.1.tar.gz

StartedAt: 2015-10-08 22:37:44 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:44:34 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 409.9 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/diffHic.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [43s/44s] 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 ... [59s/60s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
normalizeCNV 17.765  0.111  17.892
cutGenome     8.495  0.218   9.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-basic.R’ [17s/17s]
  Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ...6d5
< Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
 [18s/18s] 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c check_input.cpp -o check_input.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cluster_2d.cpp -o cluster_2d.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c count_connect.cpp -o count_connect.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c count_marginals.cpp -o count_marginals.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c count_patch.cpp -o count_patch.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.cpp -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c iterative_correction.cpp -o iterative_correction.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pair_stats.cpp -o pair_stats.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c quadrant_bg.cpp -o quadrant_bg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c report_hic_pairs.cpp -o report_hic_pairs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c trended_filter.cpp -o trended_filter.o
llvm-g++-4.2 -arch x86_64 -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 -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.294	0.002	0.296
DNaseHiC	2.231	0.093	2.352
boxPairs	0.891	0.026	0.921
clusterPairs	0.663	0.005	0.669
connectCounts	1.802	0.024	1.828
consolidatePairs	0.668	0.004	0.672
correctedContact	0.125	0.009	0.133
cutGenome	8.495	0.218	9.325
diffHicUsersGuide	0.002	0.000	0.002
enrichedPairs	0.328	0.011	0.339
filterPeaks	0.121	0.000	0.122
filters	0.061	0.000	0.062
getArea	0.222	0.004	0.227
getDistance	0.036	0.003	0.038
getPairData	0.151	0.021	0.172
loadData	0.168	0.021	0.198
marginCounts	1.418	0.025	1.454
mergePairs	0.407	0.035	0.442
normalizeCNV	17.765	0.111	17.892
pairParam	0.108	0.002	0.109
plotDI	0.972	0.010	1.033
plotPlaid	2.571	0.034	2.609
preparePairs	0.336	0.070	0.419
prunePairs	0.423	0.036	0.462
savePairs	0.140	0.006	0.154
squareCounts	1.797	0.028	1.833
totalCounts	1.212	0.030	1.246