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BioC 3.1: CHECK report for VanillaICE on zin2

This page was generated on 2015-10-09 09:23:27 -0700 (Fri, 09 Oct 2015).

Package 1002/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VanillaICE 1.30.1
Robert Scharpf
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/VanillaICE
Last Changed Rev: 104079 / Revision: 109384
Last Changed Date: 2015-05-21 17:33:04 -0700 (Thu, 21 May 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VanillaICE
Version: 1.30.1
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.30.1.tar.gz
StartedAt: 2015-10-09 06:12:27 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:15:39 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 192.5 seconds
RetCode: 0
Status:  OK 
CheckDir: VanillaICE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.30.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/VanillaICE.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.30.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doMPI’ ‘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 ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg18’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘GenomicRanges:::.ShallowSimpleListAssays’
  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 ... [14s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [30s/30s]
 [30s/30s] 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.


VanillaICE.Rcheck/00install.out:

* installing *source* package ‘VanillaICE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rinit.c -o rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (VanillaICE)

VanillaICE.Rcheck/VanillaICE-Ex.timings:

nameusersystemelapsed
ArrayViews-class2.5310.1342.663
CopyNumScanParams0.0020.0000.002
EmissionParam-methods0.010.000.01
FilterParam-class0.0020.0000.002
HMM0.1960.0000.196
HMMList-class0.4130.0000.413
HmmGRanges0.0000.0000.001
HmmParam0.0040.0000.004
IO0.0080.0000.008
IdiogramParams-class0.2260.0000.226
SnpArrayExperiment-class0.0390.0000.039
SnpExperiment0.0180.0000.018
SnpGRanges0.0250.0000.025
TransitionParam0.0010.0000.001
cnvFilter0.7630.0000.763
constraints0.0010.0000.000
dropDuplicatedMapLocs0.0810.0000.081
emissionParam0.0100.0000.011
getExampleSnpExperiment0.0010.0000.000
getHmmParams0.0090.0000.010
hmm20.5110.0000.511
icePlatforms000
isHeterozygous0.2310.0080.239
parseSourceFile0.8150.0000.815
plotting0.9730.0160.995
robust-statistics0.0000.0000.001
snpArrayAssays0.0080.0000.007
sourcePaths0.0080.0000.007
sweepMode0.1870.0000.187
threshold0.0010.0000.001
viewports0.0020.0000.002