BioC 3.4: CHECK report for diffHic on zin1
This page was generated on 2016-09-21 03:39:52 -0700 (Wed, 21 Sep 2016).
diffHic 1.5.5
Aaron Lun
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/diffHic | | Last Changed Rev: 120744 / Revision: 121152 | | Last Changed Date: 2016-09-06 03:51:50 -0700 (Tue, 06 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: diffHic |
| Version: 1.5.5 |
| Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.5.5.tar.gz |
| StartedAt: 2016-09-20 05:35:58 -0700 (Tue, 20 Sep 2016) |
| EndedAt: 2016-09-20 05:39:55 -0700 (Tue, 20 Sep 2016) |
| EllapsedTime: 236.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffHic.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.5.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/diffHic.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.5.5’
* 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 ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 2.0Mb
libs 2.4Mb
* 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 8.48 0.008 8.487
cutGenome 4.94 0.096 5.089
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.4-bioc/meat/diffHic.Rcheck/00check.log’
for details.
diffHic.Rcheck/00install.out:
* installing *source* package ‘diffHic’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c binner.cpp -o binner.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c check_input.cpp -o check_input.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c cluster_2d.cpp -o cluster_2d.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c count_background.cpp -o count_background.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c count_connect.cpp -o count_connect.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c count_patch.cpp -o count_patch.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c directionality.cpp -o directionality.o
directionality.cpp: In function ‘SEXPREC* directionality(SEXP, SEXP, SEXP, SEXP, SEXP)’:
directionality.cpp:48:9: warning: unused variable ‘current_average’ [-Wunused-variable]
double current_average;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c iterative_correction.cpp -o iterative_correction.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c nb_average.cpp -o nb_average.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c neighbors.cpp -o neighbors.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c pair_stats.cpp -o pair_stats.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c quadrant_bg.cpp -o quadrant_bg.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c report_hic_pairs.cpp -o report_hic_pairs.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c trended_filter.cpp -o trended_filter.o
g++ -shared -L/home/biocbuild/bbs-3.4-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 nb_average.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o -L/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/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 | 0.632 | 0.012 | 0.645 |
|
| annotatePairs | 0.256 | 0.004 | 0.271 |
|
| boxPairs | 0.884 | 0.012 | 0.896 |
|
| clusterPairs | 0.500 | 0.004 | 0.505 |
|
| compartmentalize | 0.288 | 0.008 | 0.294 |
|
| connectCounts | 0.804 | 0.000 | 0.806 |
|
| consolidatePairs | 0.268 | 0.000 | 0.271 |
|
| correctedContact | 0.224 | 0.000 | 0.223 |
|
| cutGenome | 4.940 | 0.096 | 5.089 |
|
| diClusters | 1.420 | 0.000 | 1.422 |
|
| diffHicUsersGuide | 0.000 | 0.000 | 0.001 |
|
| domainDirections | 0.132 | 0.000 | 0.130 |
|
| enrichedPairs | 0.052 | 0.000 | 0.053 |
|
| filterDiag | 0.136 | 0.000 | 0.136 |
|
| filterPeaks | 0.044 | 0.000 | 0.044 |
|
| filters | 0.104 | 0.000 | 0.103 |
|
| getArea | 0.100 | 0.004 | 0.102 |
|
| getPairData | 0.072 | 0.004 | 0.075 |
|
| loadData | 0.096 | 0.000 | 0.096 |
|
| marginCounts | 0.616 | 0.004 | 0.621 |
|
| mergePairs | 0.324 | 0.012 | 0.339 |
|
| neighborCounts | 0.468 | 0.004 | 0.472 |
|
| normalizeCNV | 8.480 | 0.008 | 8.487 |
|
| pairParam | 0.060 | 0.000 | 0.062 |
|
| plotDI | 0.348 | 0.004 | 0.355 |
|
| plotPlaid | 1.136 | 0.004 | 1.204 |
|
| preparePairs | 0.248 | 0.016 | 0.266 |
|
| prunePairs | 0.636 | 0.008 | 0.653 |
|
| savePairs | 0.112 | 0.004 | 0.114 |
|
| squareCounts | 1.252 | 0.004 | 1.559 |
|
| totalCounts | 0.888 | 0.004 | 1.017 |
|