BioC 3.2: CHECK report for GeneSelectMMD on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneSelectMMD_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneSelectMMD.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneSelectMMD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneSelectMMD’ version ‘2.14.0’
* 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 ‘GeneSelectMMD’ can be installed ... [7s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
obtainResi: no visible global function definition for ‘pData’
obtainResi: no visible global function definition for ‘exprs<-’
obtainResi: no visible global function definition for ‘pData<-’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘GeneSelectMMD/libs/GeneSelectMMD.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘lbfgsb.o’, ‘llkhFun.o’, ‘wiFun.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 ... [3s/3s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneSelectMMD.Rcheck/00check.log’
for details.

* installing *source* package ‘GeneSelectMMD’ ...
** libs
gfortran-4.8   -fPIC  -g -O2 -Wall  -c Qfunc.f -o Qfunc.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c blas.f -o blas.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c isnan.c -o isnan.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c lbfgsb.f -o lbfgsb.o
lbfgsb.f: In function ‘cauchy’:
lbfgsb.f:1453:0: warning: ‘tu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             xupper = nbd(i) .ge. 2 .and. tu .le. zero
 ^
lbfgsb.f:1482:0: warning: ‘tl’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                t(nbreak) = tl/(-neggi)
 ^
gfortran-4.8   -fPIC  -g -O2 -Wall  -c lbfgsbDriver.f -o lbfgsbDriver.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c linpack.f -o linpack.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c llkhFun.f -o llkhFun.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c myTtest.f -o myTtest.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c paraEstLoop.f -o paraEstLoop.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c pt.c -o pt.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c timer.f -o timer.o
gfortran-4.8   -fPIC  -g -O2 -Wall  -c wiFun.f -o wiFun.o
clang -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 GeneSelectMMD.so Qfunc.o blas.o isnan.o lbfgsb.o lbfgsbDriver.o linpack.o llkhFun.o myTtest.o paraEstLoop.o pt.o timer.o wiFun.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/GeneSelectMMD.Rcheck/GeneSelectMMD/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 (GeneSelectMMD)

name	user	system	elapsed
errRates	0.001	0.000	0.001
gsMMD	1.613	0.073	1.887
gsMMD.default	0.001	0.000	0.002
gsMMD2	0.002	0.001	0.002
gsMMD2.default	0.001	0.000	0.001
plotHistDensity	0.002	0.000	0.002

BioC 3.2: CHECK report for GeneSelectMMD on oaxaca

Summary

Command output