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BioC 2.14: CHECK report for rqubic on zin2

This page was generated on 2014-10-08 08:49:14 -0700 (Wed, 08 Oct 2014).

Package 685/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rqubic 1.10.0
Jitao David Zhang
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/rqubic
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: rqubic
Version: 1.10.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings rqubic_1.10.0.tar.gz
StartedAt: 2014-10-08 02:33:40 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:34:23 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 42.3 seconds
RetCode: 0
Status:  OK 
CheckDir: rqubic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings rqubic_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/rqubic.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rqubic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rqubic’ version ‘1.10.0’
* 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 ‘rqubic’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘biclust’
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
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘c_output_parser_tests.R’ [1s/1s]
  Running ‘rqubic_implementations.R’ [2s/2s]
  Running ‘test_read.R’ [1s/1s]
  Running ‘test_utilities.R’ [0s/0s]
 [5s/5s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/rqubic.Rcheck/00check.log’
for details.

rqubic.Rcheck/00install.out:

* installing *source* package ‘rqubic’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bicluster.c -o bicluster.o
bicluster.c: In function ‘seed_intersect_r’:
bicluster.c:354:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c discretize.c -o discretize.o
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fib.c -o fib.o
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rqubic.c -o rqubic.o
rqubic.h:60:20: warning: ‘EDGELIST_ATT_NAME’ defined but not used [-Wunused-variable]
rqubic.h:61:20: warning: ‘MINCOL_ATT_NAME’ defined but not used [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o rqubic.so bicluster.o discretize.o fib.o graph.o rqubic.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/rqubic.Rcheck/rqubic/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 (rqubic)

rqubic.Rcheck/rqubic-Ex.timings:

nameusersystemelapsed
QUBICBiclusterSet-class0.0040.0000.001
combineBiclusts-methods1.4200.0121.432
discretize0.0320.0000.031
eSetDimName0.1320.0000.133
fcFilter0.4880.0040.494
features-methods0.080.000.08
generateSeeds-methods0.0680.0080.075
parseQubicBlocks0.0960.0040.097
quBicluster0.4840.0000.485
readBiclusterResults0.0160.0040.029
writeQubicInputFile0.0440.0000.044