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BioC 3.5: CHECK report for NuPoP on malbec2

This page was generated on 2017-10-18 14:13:49 -0400 (Wed, 18 Oct 2017).

Package 910/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NuPoP 1.26.1
Ji-Ping Wang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/NuPoP
Branch: RELEASE_3_5
Last Commit: 04c1e3d
Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: NuPoP
Version: 1.26.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NuPoP_1.26.1.tar.gz
StartedAt: 2017-10-18 01:13:23 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:13:53 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 30.6 seconds
RetCode: 0
Status:  OK 
CheckDir: NuPoP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NuPoP_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/NuPoP.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-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 ‘1.26.1’
* 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 ... 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 ... NOTE
plotNuPoP: no visible global function definition for ‘par’
plotNuPoP: no visible global function definition for ‘plot’
plotNuPoP: no visible global function definition for ‘title’
plotNuPoP: no visible global function definition for ‘polygon’
plotNuPoP: no visible global function definition for ‘points’
readNuPoP: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par plot points polygon read.table title
Consider adding
  importFrom("graphics", "par", "plot", "points", "polygon", "title")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/NuPoP.Rcheck/00check.log’
for details.


NuPoP.Rcheck/00install.out:

* 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/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o NuPoP.so vtbfb.o vtbfbNL4.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)

NuPoP.Rcheck/NuPoP-Ex.timings:

nameusersystemelapsed
NuPoP-package4.5560.0204.577
plotNuPoP0.0760.0000.075
predNuPoP4.2440.0004.249
readNuPoP4.2720.0164.290