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BioC 3.2: CHECK report for NuPoP on oaxaca

This page was generated on 2015-10-27 17:39:16 -0400 (Tue, 27 Oct 2015).

Package 717/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NuPoP 1.20.0
Ji-Ping Wang
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/NuPoP
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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 06:13:12 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 06:13:46 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 33.8 seconds
RetCode: 0
Status:  OK 
CheckDir: NuPoP.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/NuPoP.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [3s/4s] 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 ... [18s/18s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
readNuPoP     6.112  0.022   6.148
predNuPoP     5.819  0.020   5.842
NuPoP-package 5.423  0.031   5.492
* 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.


NuPoP.Rcheck/00install.out:

* installing *source* package ‘NuPoP’ ...
** libs
gfortran-4.8  -fno-common -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)
vtbfb.f90: In function ‘vtbfb’:
vtbfb.f90:224:0: warning: ‘tp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         tp=tranL(w(t-d+1),w(t-d+2))*tranL(c(z-t+d-1),c(z-t+d))/r(t-d+1)*tp
 ^
gfortran-4.8  -fno-common -Wall -g -O2  -c  vtbfbNL4.f90 -o vtbfbNL4.o
vtbfbNL4.f90:257.106:

L2(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)
vtbfbNL4.f90:272.13:

      end if 
             1
Warning: Nonconforming tab character at (1)
vtbfbNL4.f90:301.107:

2(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)
vtbfbNL4.f90:314.23:

      tempL=tempL+temp 
                       1
Warning: Nonconforming tab character at (1)
vtbfbNL4.f90:335.87:

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)
vtbfbNL4.f90:364.105:

nL2(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)
vtbfbNL4.f90:15.32:

  character*80 seqName,out1,out2; character*2 tpc
                                1
Warning: Unused variable 'out2' declared at (1)
gfortran-4.8 -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 /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)

NuPoP.Rcheck/NuPoP-Ex.timings:

nameusersystemelapsed
NuPoP-package5.4230.0315.492
plotNuPoP0.0760.0030.084
predNuPoP5.8190.0205.842
readNuPoP6.1120.0226.148