Multiple platform build/check report for BioC 3.7 - CHECK report for NuPoP on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NuPoP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NuPoP_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/NuPoP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.30.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  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 ... 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
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/NuPoP/libs/NuPoP.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
readNuPoP     7.212  0.024   7.313
predNuPoP     7.168  0.027   7.273
NuPoP-package 7.143  0.045   7.252
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/NuPoP.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NuPoP
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘NuPoP’ ...
** libs
gfortran  -fPIC -Wall -g -O2  -c  vtbfb.f90 -o vtbfb.o
vtbfb.f90:13:32:

   character*80 seqName,out1,out2; character*2 tpc
                                1
Warning: Unused variable ‘out2’ declared at (1) [-Wunused-variable]
gfortran  -fPIC -Wall -g -O2  -c  vtbfbNL4.f90 -o vtbfbNL4.o
vtbfbNL4.f90:257:106:

         if(d>=3) temp=temp*tranL2(w(t-d+1),w(t-d+2),w(t-d+3))*tranL2(c(z-t+1),c(z-t+2),c(z-t+3))/r(t-d+2)   
                                                                                                          1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:272:13:

       end if 
             1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:301:107:

         if(d>=3) temp=temp*tranL2(w(t-d+1),w(t-d+2),w(t-d+3))*tranL2(c(z-t+1),c(z-t+2),c(z-t+3))/ra(t-d+2)   
                                                                                                           1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:314:23:

       tempL=tempL+temp 
                       1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:335:87:

     if(z-t>=3) rb(t)=rb(t)*tranL2(w(t+1),w(t+2),w(t+3))*tranL2(c(1),c(2),c(3))/rb(t+2)   
                                                                                       1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:364:105:

         if(d>=3) temp=temp*tranL2(w(t+1),w(t+2),w(t+3))*tranL2(c(z-t-d+1),c(z-t-d+2),c(z-t-d+3))/rb(t+2)   
                                                                                                         1
Warning: Nonconforming tab character at (1) [-Wtabs]
vtbfbNL4.f90:15:32:

   character*80 seqName,out1,out2; character*2 tpc
                                1
Warning: Unused variable ‘out2’ declared at (1) [-Wunused-variable]
gfortran -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 -o NuPoP.so vtbfb.o vtbfbNL4.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/NuPoP/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NuPoP)

CHECK report for NuPoP on merida2

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
NuPoP-package	7.143	0.045	7.252
plotNuPoP	0.059	0.003	0.062
predNuPoP	7.168	0.027	7.273
readNuPoP	7.212	0.024	7.313