Package: PICS

Version: 1.6.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings PICS_1.6.0.tar.gz

StartedAt: 2011-10-20 13:56:33 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:58:34 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 121.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PICS.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/PICS.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PICS’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘PICS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
PICS: no visible global function definition for ‘mclapply’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions/methods with usage in documentation object 'pics' but not in code:
  pics

Functions/methods with usage in documentation object 'segReadsList' but not in code:
  new

Functions/methods with usage in documentation object 'segReads' but not in code:
  new

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'segReadsList':
  new

Objects in \usage without \alias in documentation object 'segReads':
  new

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/PICS.Rcheck/00check.log’
for details

* installing *source* package ‘PICS’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c background.c -o background.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c pics.c -o pics.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c segment.c -o segment.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o PICS.so background.o pics.o segment.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/PICS.Rcheck/PICS/libs
** R
** inst
** preparing package for lazy loading
in method for ‘as.list’ with signature ‘"AlignedRead"’: no definition for class "AlignedRead"
in method for ‘coerce’ with signature ‘"AlignedRead","GenomeData"’: no definition for class "AlignedRead"
Creating a new generic function for "density" in "PICS"
Creating a new generic function for "plot" in "PICS"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (PICS)

name	user	system	elapsed
makeRangedDataOutput	0.000	0.000	0.001
pics-class	0	0	0
picsError-class	0.000	0.000	0.002
picsFDR	0	0	0
picsList-class	0	0	0
segmentReads	4.104	0.048	4.152
setParaEM	0	0	0
setParaPrior	0.000	0.000	0.001