Multiple platform build/check report for BioC 3.11 - 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_2.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneSelectMMD.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.31.0’
* 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/4.0/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-3.11-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/4.0/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/4.0/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	0.001	0.001
gsMMD	1.645	0.151	1.806
gsMMD.default	0.000	0.001	0.001
gsMMD2	0.001	0.001	0.001
gsMMD2.default	0.000	0.000	0.001
plotHistDensity	0.000	0.000	0.001

CHECK report for GeneSelectMMD on celaya2

Summary

Command output

Installation output

Tests output

Example timings