BioC 3.2: CHECK report for NuPoP on perceval

Package: NuPoP

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NuPoP_1.20.0.tar.gz

StartedAt: 2015-10-27 10:34:38 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 10:35:29 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 51.8 seconds

RetCode: 0

Status:  OK

CheckDir: NuPoP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NuPoP_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/NuPoP.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.20.0’
* 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 ... [4s/5s] OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  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 loading without being on the library search path ... 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 compiled code ... NOTE
File ‘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, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
readNuPoP     10.121  0.094  10.238
NuPoP-package  9.981  0.112  10.157
predNuPoP      9.991  0.085  10.094
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/NuPoP.Rcheck/00check.log’
for details.

* installing *source* package ‘NuPoP’ ...
** libs
gfortran-4.2 -arch x86_64  -fPIC -g -O2  -c  vtbfb.f90 -o vtbfb.o
gfortran-4.2 -arch x86_64  -fPIC -g -O2  -c  vtbfbNL4.f90 -o vtbfbNL4.o
gfortran-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o NuPoP.so vtbfb.o vtbfbNL4.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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	9.981	0.112	10.157
plotNuPoP	0.075	0.004	0.081
predNuPoP	9.991	0.085	10.094
readNuPoP	10.121	0.094	10.238