NuPoP 1.24.0
Ji-Ping Wang
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/NuPoP | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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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_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/NuPoP.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.24.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
NuPoP-package 6.016 0.039 6.062
readNuPoP 5.997 0.020 6.028
predNuPoP 5.626 0.017 5.648
* 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-3.4-bioc/meat/NuPoP.Rcheck/00check.log’
for details.
* installing *source* package ‘NuPoP’ ...
** libs
gfortran-4.8 -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)
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 -fPIC -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-3.4-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)