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BioC 3.3: CHECK report for AneuFinder on zin2

This page was generated on 2016-10-13 12:46:34 -0700 (Thu, 13 Oct 2016).

Package 41/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.0.3
Aaron Taudt
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AneuFinder
Last Changed Rev: 118048 / Revision: 122332
Last Changed Date: 2016-06-01 05:06:42 -0700 (Wed, 01 Jun 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AneuFinder
Version: 1.0.3
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AneuFinder_1.0.3.tar.gz
StartedAt: 2016-10-12 23:24:41 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:30:46 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 365.1 seconds
RetCode: 0
Status:  OK 
CheckDir: AneuFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AneuFinder_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AneuFinder.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 ‘AneuFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AneuFinder’ version ‘1.0.3’
* 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 ‘AneuFinder’ 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 ... NOTE
Aneufinder: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
simulateReads       42.862  0.951  43.970
heatmapAneuploidies 30.640  0.032  30.707
correctGC           25.538  1.293  30.784
findSCEs            23.182  0.024  24.043
getSCEcoordinates   23.167  0.028  24.024
heatmapGenomewide   20.369  0.032  20.414
findCNVs            11.441  0.159  12.222
variableWidthBins    6.874  0.048   7.475
binReads             5.861  0.028   6.378
collapseBins         5.130  0.051   5.679
subsetByCNVprofile   5.131  0.004   5.132
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.3-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.


AneuFinder.Rcheck/00install.out:

* installing *source* package ‘AneuFinder’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c loghmm.cpp -o loghmm.o
loghmm.cpp:320:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
loghmm.cpp:480:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
loghmm.cpp:518:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 ^
loghmm.cpp:583:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
scalehmm.cpp:400:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
scalehmm.cpp:694:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
scalehmm.cpp:732:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 ^
scalehmm.cpp:791:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/AneuFinder.Rcheck/AneuFinder/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 (AneuFinder)

AneuFinder.Rcheck/AneuFinder-Ex.timings:

nameusersystemelapsed
Aneufinder0.0010.0000.000
bam2GRanges0.5990.0160.615
bed2GRanges3.6060.0244.251
binReads5.8610.0286.378
blacklist2.6770.0083.197
clusterByQuality1.3830.0081.391
collapseBins5.1300.0515.679
colors0.0150.0000.016
correctGC25.538 1.29330.784
export000
filterSegments0.4030.0040.417
findCNVs11.441 0.15912.222
findSCEs23.182 0.02424.043
fixedWidthBins1.2150.0041.781
getSCEcoordinates23.167 0.02824.024
heatmapAneuploidies30.640 0.03230.707
heatmapGenomewide20.369 0.03220.414
importBed2.1680.0002.168
karyotypeMeasures4.1690.0084.182
loadGRangesFromFiles0.0000.0000.001
loadHmmsFromFiles3.0790.0083.097
simulateReads42.862 0.95143.970
subsetByCNVprofile5.1310.0045.132
variableWidthBins6.8740.0487.475