Multiple platform build/check report for BioC 3.9 - CHECK report for GeneSelectMMD on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneSelectMMD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneSelectMMD_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelectMMD.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.28.0’
* 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 ... 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<-’
optimalLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  exprs<- optimize pData pData<-
Consider adding
  importFrom("stats", "optimize")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/GeneSelectMMD/libs/GeneSelectMMD.so’:
  Found ‘__gfortran_st_open’, possibly from ‘open’ (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
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelectMMD.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 GeneSelectMMD
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GeneSelectMMD’ ...
** using staged installation
** libs
gfortran  -fPIC  -Wall -g -O2  -c Qfunc.f -o Qfunc.o
gfortran  -fPIC  -Wall -g -O2  -c blas.f -o blas.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c isnan.c -o isnan.o
gfortran  -fPIC  -Wall -g -O2  -c lbfgsb.f -o lbfgsb.o
lbfgsb.f:1491:0:

                t(nbreak) = tu/neggi
 
Warning: ‘tu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lbfgsb.f:1482:0:

                t(nbreak) = tl/(-neggi)
 
Warning: ‘tl’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fPIC  -Wall -g -O2  -c lbfgsbDriver.f -o lbfgsbDriver.o
gfortran  -fPIC  -Wall -g -O2  -c linpack.f -o linpack.o
gfortran  -fPIC  -Wall -g -O2  -c llkhFun.f -o llkhFun.o
gfortran  -fPIC  -Wall -g -O2  -c myTtest.f -o myTtest.o
gfortran  -fPIC  -Wall -g -O2  -c paraEstLoop.f -o paraEstLoop.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pt.c -o pt.o
gfortran  -fPIC  -Wall -g -O2  -c timer.f -o timer.o
gfortran  -fPIC  -Wall -g -O2  -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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for _lbfgsbdriver_: stack subq instruction is too different from dwarf stack size
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-GeneSelectMMD/00new/GeneSelectMMD/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneSelectMMD)

name	user	system	elapsed
errRates	0.000	0.000	0.001
gsMMD	1.539	0.133	1.675
gsMMD.default	0	0	0
gsMMD2	0.001	0.001	0.001
gsMMD2.default	0.000	0.001	0.001
plotHistDensity	0.000	0.001	0.001

CHECK report for GeneSelectMMD on celaya2

Summary

Command output

Installation output

Tests output

Example timings