GeneSelectMMD 2.17.0
Weiliang Qiu
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneSelectMMD | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GeneSelectMMD_2.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GeneSelectMMD.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘2.17.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: ‘tu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
Warning: ‘tl’ may be used uninitialized in this function [-Wmaybe-uninitialized]
See ‘/home/biocbuild/bbs-3.4-bioc/meat/GeneSelectMMD.Rcheck/00install.out’ for details.
* 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 ... 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 ... 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/GeneSelectMMD.Rcheck/00check.log’
for details.
* installing *source* package ‘GeneSelectMMD’ ...
** libs
f95 -fpic -g -O2 -Wall -c Qfunc.f -o Qfunc.o
f95 -fpic -g -O2 -Wall -c blas.f -o blas.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c isnan.c -o isnan.o
f95 -fpic -g -O2 -Wall -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]
f95 -fpic -g -O2 -Wall -c lbfgsbDriver.f -o lbfgsbDriver.o
f95 -fpic -g -O2 -Wall -c linpack.f -o linpack.o
f95 -fpic -g -O2 -Wall -c llkhFun.f -o llkhFun.o
f95 -fpic -g -O2 -Wall -c myTtest.f -o myTtest.o
f95 -fpic -g -O2 -Wall -c paraEstLoop.f -o paraEstLoop.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pt.c -o pt.o
f95 -fpic -g -O2 -Wall -c timer.f -o timer.o
f95 -fpic -g -O2 -Wall -c wiFun.f -o wiFun.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/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 -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)