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BioC 3.1: CHECK report for GeneSelectMMD on petty

This page was generated on 2015-10-09 09:33:49 -0700 (Fri, 09 Oct 2015).

Package 384/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneSelectMMD 2.12.0
Weiliang Qiu
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GeneSelectMMD
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneSelectMMD
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneSelectMMD_2.12.0.tar.gz
StartedAt: 2015-10-08 23:13:12 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:14:20 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 67.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneSelectMMD.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneSelectMMD_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GeneSelectMMD.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.12.0’
* 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 ... [9s/9s] 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 loading without being on the library search path ... 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 ... [4s/4s] 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-3.1-bioc/meat/GeneSelectMMD.Rcheck/00check.log’
for details.


GeneSelectMMD.Rcheck/00install.out:

* installing *source* package ‘GeneSelectMMD’ ...
** libs
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c Qfunc.f -o Qfunc.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c blas.f -o blas.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c isnan.c -o isnan.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c lbfgsb.f -o lbfgsb.o
lbfgsb.f: In function ‘cauchy’:
lbfgsb.f:1409: warning: ‘tl’ may be used uninitialized in this function
lbfgsb.f:1409: warning: ‘tu’ may be used uninitialized in this function
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c lbfgsbDriver.f -o lbfgsbDriver.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c linpack.f -o linpack.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c llkhFun.f -o llkhFun.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c myTtest.f -o myTtest.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c paraEstLoop.f -o paraEstLoop.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pt.c -o pt.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c timer.f -o timer.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall  -c wiFun.f -o wiFun.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-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)

GeneSelectMMD.Rcheck/GeneSelectMMD-Ex.timings:

nameusersystemelapsed
errRates0.0010.0000.002
gsMMD2.1560.1412.301
gsMMD.default0.0010.0000.002
gsMMD20.0030.0000.003
gsMMD2.default0.0030.0010.003
plotHistDensity0.0020.0010.002