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BioC 3.5: CHECK report for VanillaICE on malbec2

This page was generated on 2017-08-16 13:12:59 -0400 (Wed, 16 Aug 2017).

Package 1354/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VanillaICE 1.38.0
Robert Scharpf
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/VanillaICE
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  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VanillaICE
Version: 1.38.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.38.0.tar.gz
StartedAt: 2017-08-16 02:50:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:54:01 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 235.7 seconds
RetCode: 0
Status:  OK 
CheckDir: VanillaICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/VanillaICE.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 ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.38.0’
* 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 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.


VanillaICE.Rcheck/00install.out:

* installing *source* package ‘VanillaICE’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rinit.c -o rinit.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
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
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (VanillaICE)

VanillaICE.Rcheck/VanillaICE-Ex.timings:

nameusersystemelapsed
ArrayViews-class3.7560.0203.779
CopyNumScanParams0.0040.0000.004
EmissionParam-methods0.0080.0040.013
FilterParam-class0.0040.0000.004
HMM0.8040.0240.827
HMMList-class0.6960.0000.695
HmmParam0.0040.0000.003
IO0.0040.0000.006
IdiogramParams-class0.2000.0080.228
SnpArrayExperiment-class0.2480.0040.249
SnpExperiment0.0560.0000.055
SnpGRanges0.0840.0000.084
TransitionParam0.0040.0000.002
cnvFilter0.8000.0000.798
dropDuplicatedMapLocs0.1720.0000.175
emissionParam0.0160.0000.016
getExampleSnpExperiment000
getHmmParams0.0080.0000.008
hmm20.4240.0040.427
isHeterozygous0.2640.0040.282
parseSourceFile0.4960.0040.499
plotting0.9000.0120.911
robust-statistics000
snpArrayAssays0.0080.0000.009
sourcePaths0.0080.0000.006
sweepMode0.1760.0000.176
threshold000
viewports0.0080.0000.010