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BioC 3.5: CHECK report for AneuFinder on malbec2

This page was generated on 2017-08-16 13:17:26 -0400 (Wed, 16 Aug 2017).

Package 44/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.4.0
Aaron Taudt
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/AneuFinder
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AneuFinder
Version: 1.4.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AneuFinder_1.4.0.tar.gz
StartedAt: 2017-08-15 21:07:04 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:15:13 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 489.2 seconds
RetCode: 0
Status:  OK 
CheckDir: AneuFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings AneuFinder_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/AneuFinder.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.4.0’
* 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 ‘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 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             40.944 12.892  53.939
heatmapAneuploidies       38.524  0.068  38.629
correctGC                 26.880  4.264  44.232
plotHeterogeneity         22.484  0.028  22.531
getSCEcoordinates         21.268  0.040  22.866
karyotypeMeasures         17.128  0.008  17.152
findCNVs.strandseq        15.020  0.044  16.672
heatmapGenomewide         14.492  0.072  14.820
heatmapGenomewideClusters  9.992  0.036  10.037
findCNVs                   8.412  0.092  10.157
consensusSegments          5.960  0.004   5.967
subsetByCNVprofile         5.152  0.016   5.176
binReads                   5.124  0.016   7.248
collapseBins               5.048  0.040   6.826
variableWidthBins          4.668  0.092   6.468
bed2GRanges                3.480  0.024   5.699
blacklist                  3.308  0.036   5.287
* 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-3.5-bioc/meat/AneuFinder.Rcheck/00check.log’
for details.


AneuFinder.Rcheck/00install.out:

* installing *source* package ‘AneuFinder’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.5-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-3.5-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-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
Aneufinder0.0040.0000.000
bam2GRanges1.2520.0401.877
bed2GRanges3.4800.0245.699
binReads5.1240.0167.248
blacklist3.3080.0365.287
clusterByQuality1.4400.0041.523
collapseBins5.0480.0406.826
colors0.0280.0000.025
compareMethods0.4120.0040.417
consensusSegments5.9600.0045.967
correctGC26.880 4.26444.232
export0.0000.0000.001
filterSegments0.4000.0040.406
findCNVs 8.412 0.09210.157
findCNVs.strandseq15.020 0.04416.672
fixedWidthBins0.1040.0001.756
getDistinctColors0.0240.0000.025
getQC0.7480.0040.781
getSCEcoordinates21.268 0.04022.866
heatmapAneuploidies38.524 0.06838.629
heatmapGenomewide14.492 0.07214.820
heatmapGenomewideClusters 9.992 0.03610.037
importBed2.020.002.02
karyotypeMeasures17.128 0.00817.152
loadFromFiles2.6200.0002.623
plotHeterogeneity22.484 0.02822.531
plot_pca0.9240.0000.925
simulateReads40.94412.89253.939
subsetByCNVprofile5.1520.0165.176
variableWidthBins4.6680.0926.468