BioC 3.2: CHECK report for diffHic on linux1.bioconductor.org
This page was generated on 2015-10-27 17:27:12 -0400 (Tue, 27 Oct 2015).
diffHic 1.2.0
Aaron Lun
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/diffHic | | Last Changed Rev: 109616 / Revision: 109947 | | Last Changed Date: 2015-10-14 12:21:37 -0400 (Wed, 14 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: diffHic |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.2.0.tar.gz |
| StartedAt: 2015-10-27 02:57:38 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 03:02:03 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 265.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: diffHic.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings diffHic_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/diffHic.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [35s/35s] 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
normalizeCNV 12.010 0.000 12.034
cutGenome 6.192 0.056 6.262
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-basic.R’ [11s/11s]
Comparing ‘test-basic.Rout’ to ‘test-basic.Rout.save’ ... OK
[11s/11s] 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-3.2-bioc/meat/diffHic.Rcheck/00check.log’
for details.
diffHic.Rcheck/00install.out:
* installing *source* package ‘diffHic’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c binner.cpp -o binner.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c check_input.cpp -o check_input.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cluster_2d.cpp -o cluster_2d.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_background.cpp -o count_background.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_connect.cpp -o count_connect.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_patch.cpp -o count_patch.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c directionality.cpp -o directionality.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c iterative_correction.cpp -o iterative_correction.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nb_average.cpp -o nb_average.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c neighbors.cpp -o neighbors.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pair_stats.cpp -o pair_stats.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c quadrant_bg.cpp -o quadrant_bg.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c report_hic_pairs.cpp -o report_hic_pairs.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c trended_filter.cpp -o trended_filter.o
g++ -shared -L/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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
|
| DIList | 0.538 | 0.004 | 0.542 |
|
| DNaseHiC | 1.003 | 0.024 | 1.033 |
|
| boxPairs | 0.942 | 0.000 | 0.943 |
|
| clusterPairs | 0.439 | 0.004 | 0.445 |
|
| compartmentalize | 0.194 | 0.000 | 0.194 |
|
| connectCounts | 0.760 | 0.000 | 0.761 |
|
| consolidatePairs | 0.287 | 0.000 | 0.287 |
|
| correctedContact | 0.18 | 0.00 | 0.18 |
|
| cutGenome | 6.192 | 0.056 | 6.262 |
|
| diffHicUsersGuide | 0.001 | 0.000 | 0.001 |
|
| domainDirections | 0.258 | 0.012 | 0.270 |
|
| enrichedPairs | 0.029 | 0.000 | 0.030 |
|
| filterDiag | 0.130 | 0.004 | 0.134 |
|
| filterPeaks | 0.022 | 0.000 | 0.021 |
|
| filters | 0.065 | 0.000 | 0.066 |
|
| getArea | 0.101 | 0.000 | 0.100 |
|
| getDistance | 0.007 | 0.008 | 0.015 |
|
| getPairData | 0.060 | 0.000 | 0.059 |
|
| loadData | 0.061 | 0.004 | 0.065 |
|
| marginCounts | 0.812 | 0.000 | 0.812 |
|
| mergePairs | 0.242 | 0.000 | 0.243 |
|
| neighborCounts | 0.361 | 0.004 | 0.365 |
|
| normalizeCNV | 12.010 | 0.000 | 12.034 |
|
| pairParam | 0.097 | 0.000 | 0.099 |
|
| plotDI | 0.670 | 0.000 | 0.672 |
|
| plotPlaid | 1.714 | 0.000 | 1.714 |
|
| preparePairs | 0.203 | 0.000 | 0.204 |
|
| prunePairs | 0.266 | 0.008 | 0.276 |
|
| savePairs | 0.064 | 0.000 | 0.064 |
|
| squareCounts | 1.246 | 0.004 | 1.250 |
|
| totalCounts | 0.536 | 0.000 | 0.537 |
|
| wrappers | 0.029 | 0.000 | 0.029 |
|