Package: mgsa

Version: 1.7.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings mgsa_1.7.0.tar.gz

StartedAt: 2013-01-16 04:19:25 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 04:20:16 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 51.8 seconds

RetCode: 0

Status:  OK

CheckDir: mgsa.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/mgsa.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mgsa/DESCRIPTION’ ... OK
* this is package ‘mgsa’ version ‘1.7.0’
* 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 ‘mgsa’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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
File ‘mgsa/R/zzz.R’:
  .First.lib calls:
    print(paste(lib, pkg))
    print(paste("Package mgsa initialized"))

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

plot,MgsaResults: warning in close.screen(all = T): partial argument
  match of 'all' to 'all.screens'
readGAF: no visible binding for global variable ‘aspect.code’
readGAF: no visible binding for global variable ‘evidence.code’
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/mgsa.Rcheck/mgsa/libs/mgsa.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘mgsa.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
readGAF      6.648  0.144   7.032
mgsa-methods 6.704  0.004   3.732
* 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

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/mgsa.Rcheck/00check.log’
for details.

* installing *source* package ‘mgsa’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for OpenMP flag of C compiler... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -g -O2 -fopenmp -DPACKAGE_NAME=\"mgsa\" -DPACKAGE_TARNAME=\"mgsa\" -DPACKAGE_VERSION=\"0.99.0\" -DPACKAGE_STRING=\"mgsa\ 0.99.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_OPENMP=1 -I/usr/local/include    -fpic  -g -O2  -c mgsa.c -o mgsa.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o mgsa.so mgsa.o -fopenmp -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/mgsa.Rcheck/mgsa/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘mgsa’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘mgsa.Rnw’ 
** testing if installed package can be loaded

* DONE (mgsa)

name	user	system	elapsed
MgsaSets-class	0.012	0.004	0.018
mgsa-methods	6.704	0.004	3.732
readGAF	6.648	0.144	7.032