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BioC 3.4: CHECK report for chromstaR on morelia

This page was generated on 2017-04-15 16:27:51 -0400 (Sat, 15 Apr 2017).

Package 205/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromstaR 1.0.0
Aaron Taudt
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/chromstaR
Last Changed Rev: 123155 / Revision: 128728
Last Changed Date: 2016-10-28 13:53:44 -0400 (Fri, 28 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: chromstaR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.0.0.tar.gz
StartedAt: 2017-04-14 23:55:49 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-15 00:02:26 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 396.5 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/chromstaR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.0’
* 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 ‘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
readCustomBedFile     12.850  0.168  13.071
combineMultivariates  12.359  0.447  13.684
enrichment_analysis   12.306  0.422  19.696
transitionFrequencies  7.303  0.404  47.992
readBedFileAsGRanges   6.111  0.229   6.393
callPeaksMultivariate  5.487  0.196   5.782
Chromstar              5.090  0.224  36.126
plotExpression         2.142  0.071   7.257
* 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-3.4-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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_interface.cpp -o R_interface.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c densities.cpp -o densities.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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 5.090 0.22436.126
binReads0.2820.0230.424
callPeaksMultivariate5.4870.1965.782
callPeaksReplicates3.6020.1433.800
callPeaksUnivariate1.7760.0701.849
changePostCutoff2.8270.1142.946
collapseBins0.6880.0160.705
combinatorialStates3.7180.1063.960
combineMultivariates12.359 0.44713.684
combined_model0.2080.0160.225
conversion0.0010.0000.001
enrichment_analysis12.306 0.42219.696
experiment.table0.0040.0010.004
exportBinnedData0.3690.0270.468
exportCombinedMultivariate1.7300.0782.101
exportGRangesAsBedFile0.7520.0420.930
exportMultivariate0.7730.0440.865
exportUnivariates1.1750.0511.237
fixedWidthBins0.1340.0593.467
genomicFrequencies0.1280.0150.142
getDistinctColors0.0360.0060.485
getStateColors0.0030.0010.164
heatmapCombinations0.6400.0110.814
loadHmmsFromFiles1.7220.0541.819
multiHMM0.1220.0130.137
multivariate_model0.1220.0120.135
plotExpression2.1420.0717.257
readBamFileAsGRanges1.4060.0851.492
readBedFileAsGRanges6.1110.2296.393
readCustomBedFile12.850 0.16813.071
state.brewer0.0180.0010.018
stateBrewer0.0500.0020.052
transitionFrequencies 7.303 0.40447.992
unis2pseudomulti3.2700.1373.431
variableWidthBins3.4080.4993.912