BioC 2.13: CHECK report for NuPoP on zin1

Package: NuPoP

Version: 1.12.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings NuPoP_1.12.0.tar.gz

StartedAt: 2014-04-05 02:46:43 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:47:20 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 36.9 seconds

RetCode: 0

Status:  OK

CheckDir: NuPoP.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/NuPoP.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 ‘NuPoP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NuPoP’ version ‘1.12.0’
* 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 ‘NuPoP’ can be installed ... [3s/3s] OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
* 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 ... OK
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/NuPoP.Rcheck/NuPoP/libs/NuPoP.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘vtbfb.o’, ‘vtbfbNL4.o’

Compiled code should not call entry points 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘NuPoP-intro.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
NuPoP-package 8.288  0.024   8.344
readNuPoP     8.156  0.008   8.178
predNuPoP     8.001  0.004   8.018
* 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/NuPoP.Rcheck/00check.log’
for details.

* installing *source* package ‘NuPoP’ ...
** libs
gfortran  -fpic -g -O2  -c  vtbfb.f90 -o vtbfb.o
gfortran  -fpic -g -O2  -c  vtbfbNL4.f90 -o vtbfbNL4.o
gfortran -shared -L/usr/local/lib -o NuPoP.so vtbfb.o vtbfbNL4.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/NuPoP.Rcheck/NuPoP/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NuPoP)

name	user	system	elapsed
NuPoP-package	8.288	0.024	8.344
plotNuPoP	0.092	0.000	0.092
predNuPoP	8.001	0.004	8.018
readNuPoP	8.156	0.008	8.178