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BioC 3.6: CHECK report for chromstaR on veracruz1

This page was generated on 2017-08-16 13:49:02 -0400 (Wed, 16 Aug 2017).

Package 222/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.3.1
Aaron Taudt
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chromstaR
Last Changed Rev: 131423 / Revision: 131943
Last Changed Date: 2017-07-20 05:30:00 -0400 (Thu, 20 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: chromstaR
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.3.1.tar.gz
StartedAt: 2017-08-16 01:10:41 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:18:28 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 466.8 seconds
RetCode: 0
Status:  OK 
CheckDir: chromstaR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.3.1’
* 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 ‘chromstaR’ 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
Chromstar: 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
combineMultivariates  19.520  1.306  21.478
enrichment_analysis   13.541  0.599  17.925
callPeaksMultivariate 10.022  0.533  10.860
readCustomBedFile      9.383  0.126   9.755
Chromstar              8.693  0.291  50.575
callPeaksReplicates    7.367  0.536   8.115
transitionFrequencies  6.543  0.389  68.450
unis2pseudomulti       5.573  0.387   6.085
combinatorialStates    4.734  0.364   5.240
plotExpression         2.191  0.087   5.613
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck/00check.log’
for details.


chromstaR.Rcheck/00install.out:

* installing *source* package ‘chromstaR’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c R_interface.cpp -o R_interface.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c densities.cpp -o densities.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c utility.cpp -o utility.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 chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/chromstaR.Rcheck/chromstaR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chromstaR)

chromstaR.Rcheck/chromstaR-Ex.timings:

nameusersystemelapsed
Chromstar 8.693 0.29150.575
binReads0.6140.0280.700
callPeaksMultivariate10.022 0.53310.860
callPeaksReplicates7.3670.5368.115
callPeaksUnivariate2.3570.1522.581
changeFDR3.5050.1973.814
changePostCutoff3.4110.2263.737
collapseBins0.7840.0340.842
combinatorialStates4.7340.3645.240
combineMultivariates19.520 1.30621.478
combined_model0.1040.0170.121
conversion0.0010.0000.001
enrichment_analysis13.541 0.59917.925
experiment.table0.0030.0010.004
exportFiles0.7900.0250.826
exportGRangesAsBedFile0.8480.0440.915
fixedWidthBins0.0660.0020.073
genes_rn40.1290.0050.135
genomicFrequencies0.1460.0170.170
getCombinations0.1640.0090.173
getDistinctColors0.0290.0030.037
getStateColors0.0190.0000.018
heatmapCombinations0.4650.0110.494
heatmapCountCorrelation0.3080.0120.330
heatmapTransitionProbs0.3030.0100.326
loadHmmsFromFiles1.8160.1212.007
multiHMM0.1260.0120.145
multivariate_model0.1250.0090.138
plotExpression2.1910.0875.613
plotHistogram2.3550.1652.600
readBamFileAsGRanges0.7880.0860.894
readBedFileAsGRanges4.3880.1424.628
readCustomBedFile9.3830.1269.755
removeCondition0.7360.0920.853
state.brewer0.0130.0010.014
stateBrewer0.0420.0010.045
transitionFrequencies 6.543 0.38968.450
unis2pseudomulti5.5730.3876.085
variableWidthBins2.9860.3413.434