BioC 3.4: CHECK report for diffHic on morelia
This page was generated on 2017-04-15 16:26:31 -0400 (Sat, 15 Apr 2017).
diffHic 1.6.0
Aaron Lun
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/diffHic | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
Summary
| Package: diffHic |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffHic_1.6.0.tar.gz |
| StartedAt: 2017-04-15 01:06:40 -0700 (Sat, 15 Apr 2017) |
| EndedAt: 2017-04-15 01:12:31 -0700 (Sat, 15 Apr 2017) |
| EllapsedTime: 350.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffHic.Rcheck |
| Warnings: 0 |
Command output
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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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/diffHic.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.6.0’
* 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 10.578 0.098 10.683
cutGenome 5.571 0.140 6.300
* 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
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
directionality.cpp:48:9: warning: unused variable 'current_average' [-Wunused-variable]
double current_average;
^
1 warning generated.
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 /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.a -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-3.4-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 | 1.294 | 0.055 | 1.568 |
|
| annotatePairs | 0.368 | 0.013 | 0.381 |
|
| boxPairs | 0.830 | 0.050 | 0.884 |
|
| clusterPairs | 0.670 | 0.004 | 0.675 |
|
| compartmentalize | 0.497 | 0.010 | 0.508 |
|
| connectCounts | 1.220 | 0.013 | 1.238 |
|
| consolidatePairs | 0.511 | 0.001 | 0.514 |
|
| correctedContact | 0.291 | 0.005 | 0.298 |
|
| cutGenome | 5.571 | 0.140 | 6.300 |
|
| diClusters | 1.631 | 0.030 | 1.663 |
|
| diffHicUsersGuide | 0.001 | 0.000 | 0.001 |
|
| domainDirections | 0.185 | 0.007 | 0.192 |
|
| enrichedPairs | 0.075 | 0.000 | 0.076 |
|
| filterDiag | 0.191 | 0.005 | 0.195 |
|
| filterPeaks | 0.062 | 0.000 | 0.062 |
|
| filters | 0.142 | 0.002 | 0.143 |
|
| getArea | 0.151 | 0.002 | 0.171 |
|
| getPairData | 0.099 | 0.005 | 0.122 |
|
| loadData | 0.130 | 0.006 | 0.138 |
|
| marginCounts | 0.793 | 0.014 | 0.828 |
|
| mergePairs | 0.438 | 0.015 | 0.755 |
|
| neighborCounts | 0.605 | 0.007 | 0.613 |
|
| normalizeCNV | 10.578 | 0.098 | 10.683 |
|
| pairParam | 0.089 | 0.002 | 0.089 |
|
| plotDI | 0.520 | 0.005 | 0.526 |
|
| plotPlaid | 1.311 | 0.016 | 1.329 |
|
| preparePairs | 0.282 | 0.014 | 0.295 |
|
| prunePairs | 0.637 | 0.018 | 0.655 |
|
| savePairs | 0.124 | 0.004 | 0.128 |
|
| squareCounts | 1.189 | 0.011 | 1.201 |
|
| totalCounts | 0.888 | 0.010 | 0.903 |
|