BioC 2.13: CHECK report for VanillaICE on zin1

Package: VanillaICE

Version: 1.24.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.24.0.tar.gz

StartedAt: 2014-04-05 04:28:36 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:32:43 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 246.7 seconds

RetCode: 0

Status:  OK

CheckDir: VanillaICE.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/VanillaICE.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.24.0’
* 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 ‘VanillaICE’ can be installed ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘foreach’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  ‘grid’ ‘lattice’
  All declared Imports should be used.
Unexported object imported by a ‘:::’ call: ‘oligoClasses:::.getArm’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘initializeLrrAndBafMatrix’ ‘updateSigma’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
hmm-methods   14.345   0.12  14.654
BeadStudioSet 11.637   0.12  11.776
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [44s/44s]
 [45s/45s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/VanillaICE.Rcheck/00check.log’
for details.

* installing *source* package ‘VanillaICE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
viterbi.c: In function ‘viterbi’:
viterbi.c:108:34: warning: unused variable ‘tp’ [-Wunused-variable]
viterbi.c: At top level:
viterbi.c:244:27: warning: "/*" within comment [-Wcomment]
viterbi.c: In function ‘viterbi2’:
viterbi.c:257:3: warning: "/*" within comment [-Wcomment]
viterbi.c:262:13: warning: unused variable ‘tt’ [-Wunused-variable]
viterbi.c:260:34: warning: unused variable ‘tp’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/VanillaICE.Rcheck/VanillaICE/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 (VanillaICE)

name	user	system	elapsed
BeadStudioSet	11.637	0.120	11.776
BeadStudioSetList-methods	0.020	0.004	0.025
BeadStudioSetList	0.084	0.000	0.086
hmm-methods	14.345	0.120	14.654
hmmResults	0.000	0.000	0.002
icePlatforms	0.000	0.000	0.002
oligoSetList-methods	1.092	0.016	1.109
read.bsfiles	0.084	0.004	0.086
robustSds	0.052	0.004	0.070