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BioC 2.12: CHECK report for genefilter on petty

This page was generated on 2013-10-09 09:39:20 -0700 (Wed, 09 Oct 2013).

Package 252/671HostnameOS / ArchBUILDCHECKBUILD BIN
genefilter 1.42.0
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/genefilter
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: genefilter
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefilter_1.42.0.tar.gz
StartedAt: 2013-10-08 22:28:09 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:31:49 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 219.6 seconds
RetCode: 0
Status:  OK 
CheckDir: genefilter.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.42.0'
* 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 'genefilter' can be installed ... [19s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eSetFilter : buildGUI: no visible binding for '<<-' assignment to 'END'
eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment
  to 'END'
eSetFilter : buildGUI: no visible binding for global variable 'END'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [35s/36s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
rowFtests       12.924  0.216  13.281
half.range.mode  7.236  0.119   7.419
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RColorBrewer'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck/00check.log'
for details.

genefilter.Rcheck/00install.out:

* installing *source* package 'genefilter' ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c half_range_mode.cpp -o half_range_mode.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  -c init.c -o init.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  -c nd.c -o nd.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  -c pAUC.c -o pAUC.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  -c rowPAUCs.c -o rowPAUCs.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  -c rowttests.c -o rowttests.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c ttest.f -o ttest.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.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-2.12-bioc/meat/genefilter.Rcheck/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'genefilter'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefilter)

genefilter.Rcheck/genefilter-Ex.timings:

nameusersystemelapsed
Anova0.0300.0020.033
allNA0.0110.0010.012
coxfilter0.1420.0080.160
cv0.0070.0010.008
dist20.0210.0020.023
eSetFilter0.0100.0000.013
filter_volcano0.0040.0010.006
filtered_p0.0050.0010.005
filterfun0.0150.0010.017
findLargest1.1600.0561.262
gapFilter0.0420.0010.043
genefilter0.0260.0000.027
genefinder0.4270.0350.464
genescale0.0170.0030.020
half.range.mode7.2360.1197.419
kOverA0.0170.0020.020
kappa_p0.0100.0010.011
maxA0.0100.0010.011
nsFilter0.9350.0350.983
pOverA0.0200.0020.023
rejection_plot0.0080.0020.010
rowFtests12.924 0.21613.281
rowROC-class0.2270.0330.264
rowSds0.0050.0040.009
rowpAUCs2.7460.0602.853
shorth0.0150.0090.023
tdata0.2420.0070.250
ttest0.0220.0110.033