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BioC 3.6: CHECK report for VanillaICE on veracruz1

This page was generated on 2017-08-16 13:39:52 -0400 (Wed, 16 Aug 2017).

Package 1380/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VanillaICE 1.39.2
Robert Scharpf
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE
Last Changed Rev: 130713 / Revision: 131943
Last Changed Date: 2017-06-27 13:05:27 -0400 (Tue, 27 Jun 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: VanillaICE
Version: 1.39.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VanillaICE_1.39.2.tar.gz
StartedAt: 2017-08-16 09:24:17 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 09:28:48 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 270.9 seconds
RetCode: 0
Status:  OK 
CheckDir: VanillaICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings VanillaICE_1.39.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/VanillaICE.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 ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.39.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doRedis’
* 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 ‘VanillaICE’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BSgenome.Hsapiens.UCSC.hg18’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘SummarizedExperiment:::.ShallowSimpleListAssays0’
  See the note in ?`:::` about the use of this operator.
* 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.


VanillaICE.Rcheck/00install.out:

* installing *source* package ‘VanillaICE’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rinit.c -o rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c viterbi.c -o viterbi.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 VanillaICE.so rinit.o viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘distance’ in package ‘VanillaICE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VanillaICE)

VanillaICE.Rcheck/VanillaICE-Ex.timings:

nameusersystemelapsed
ArrayViews-class2.8740.0713.009
CopyNumScanParams0.0020.0000.002
EmissionParam-methods0.0060.0000.007
FilterParam-class0.0020.0010.002
HMM0.8440.0420.920
HMMList-class0.7960.0110.928
HmmParam0.0040.0010.009
IO0.0090.0000.010
IdiogramParams-class0.2590.0070.351
SnpArrayExperiment-class0.2100.0050.296
SnpExperiment0.0470.0000.058
SnpGRanges0.1080.0010.139
TransitionParam0.0010.0000.001
cnvFilter1.0960.0111.396
dropDuplicatedMapLocs0.2340.0060.310
emissionParam0.0220.0000.027
getExampleSnpExperiment0.0000.0000.001
getHmmParams0.0100.0000.017
hmm20.5580.0100.632
isHeterozygous0.2860.0110.316
parseSourceFile0.5660.0240.616
plotting1.7700.0342.185
robust-statistics0.0010.0000.001
snpArrayAssays0.0120.0030.015
sourcePaths0.0080.0000.008
sweepMode0.2120.0050.292
threshold0.0010.0000.002
viewports0.0140.0000.015