| Back to the "Multiple platform build/check report" | A B C [D] E F G H I J K L M N O P Q R S T U V W X Y Z |
This page was generated on 2016-04-21 13:26:35 -0700 (Thu, 21 Apr 2016).
| Package 302/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| diffHic 1.3.10 Aaron Lun
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | | |||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: diffHic |
| Version: 1.3.10 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.3.10.tar.gz |
| StartedAt: 2016-04-21 01:37:48 -0700 (Thu, 21 Apr 2016) |
| EndedAt: 2016-04-21 01:44:23 -0700 (Thu, 21 Apr 2016) |
| EllapsedTime: 395.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffHic.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.3.10.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/diffHic.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.3.10’
* 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 ... [48s/51s] 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 ... [48s/50s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
normalizeCNV 12.082 0.101 12.339
cutGenome 5.634 0.128 6.245
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-basic.R’ [15s/16s]
Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
[16s/16s] 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
diffHic.Rcheck/00install.out:
* 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 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 -L/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib -lhts -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-3.3-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)
diffHic.Rcheck/diffHic-Ex.timings:
| name | user | system | elapsed | |
| DNaseHiC | 1.113 | 0.046 | 1.391 | |
| annotatePairs | 0.507 | 0.006 | 0.514 | |
| boxPairs | 1.008 | 0.008 | 1.020 | |
| clusterPairs | 0.928 | 0.005 | 0.938 | |
| compartmentalize | 0.468 | 0.008 | 0.476 | |
| connectCounts | 1.361 | 0.014 | 1.404 | |
| consolidatePairs | 0.552 | 0.002 | 0.562 | |
| correctedContact | 0.302 | 0.007 | 0.308 | |
| cutGenome | 5.634 | 0.128 | 6.245 | |
| diClusters | 2.346 | 0.054 | 2.425 | |
| diffHicUsersGuide | 0.002 | 0.000 | 0.002 | |
| domainDirections | 0.307 | 0.009 | 0.316 | |
| enrichedPairs | 0.102 | 0.001 | 0.103 | |
| filterDiag | 0.196 | 0.006 | 0.206 | |
| filterPeaks | 0.071 | 0.000 | 0.071 | |
| filters | 0.169 | 0.001 | 0.171 | |
| getArea | 0.183 | 0.003 | 0.193 | |
| getPairData | 0.076 | 0.004 | 0.082 | |
| loadData | 0.094 | 0.006 | 0.131 | |
| marginCounts | 0.923 | 0.010 | 0.938 | |
| mergePairs | 0.281 | 0.014 | 0.300 | |
| neighborCounts | 0.741 | 0.008 | 0.820 | |
| normalizeCNV | 12.082 | 0.101 | 12.339 | |
| pairParam | 0.115 | 0.001 | 0.118 | |
| plotDI | 0.633 | 0.006 | 0.646 | |
| plotPlaid | 1.532 | 0.014 | 1.568 | |
| preparePairs | 0.131 | 0.013 | 0.144 | |
| prunePairs | 0.280 | 0.017 | 0.299 | |
| savePairs | 0.080 | 0.003 | 0.087 | |
| squareCounts | 1.193 | 0.012 | 1.215 | |
| totalCounts | 0.777 | 0.011 | 0.795 | |