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BioC 3.0: CHECK report for iClusterPlus on perceval

This page was generated on 2015-04-10 09:59:10 -0700 (Fri, 10 Apr 2015).

Package 446/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iClusterPlus 1.2.0
Qianxing Mo , Ronglai Shen
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/iClusterPlus
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: iClusterPlus
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iClusterPlus_1.2.0.tar.gz
StartedAt: 2015-04-10 02:50:22 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:53:03 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 160.6 seconds
RetCode: 0
Status:  OK 
CheckDir: iClusterPlus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iClusterPlus_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/iClusterPlus.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iClusterPlus/DESCRIPTION’ ... OK
* this is package ‘iClusterPlus’ version ‘1.2.0’
* 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 ‘iClusterPlus’ can be installed ... [20s/23s] OK
* checking installed package size ... NOTE
  installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
    doc    3.9Mb
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
classError: no visible global function definition for ‘mapClass’
CNregions: no visible binding for global variable ‘chromosome’
CNregions: no visible binding for global variable ‘num.mark’
CNregions: no visible global function definition for ‘GRanges’
CNregions: no visible global function definition for ‘IRanges’
CNregions: no visible global function definition for ‘findOverlaps’
CNregions : get.medoid: no visible global function definition for ‘pam’
plotHeatmap: no visible global function definition for ‘bluered’
plotHeatmap : my.panel.levelplot: no visible global function definition
  for ‘panel.levelplot’
plotHeatmap : my.panel.levelplot: no visible global function definition
  for ‘panel.abline’
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for ‘panel.levelplot’
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for ‘panel.abline’
plotHeatmap: no visible global function definition for ‘levelplot’
tune.iCluster2: no visible binding for global variable ‘glp’
tune.iClusterPlus: no visible binding for global variable ‘glp’
tune.iClusterPlus: no visible global function definition for ‘mclapply’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
iCluster 7.801  0.077     7.9
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [89s/89s]
 [89s/90s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/iClusterPlus.Rcheck/00check.log’
for details.

iClusterPlus.Rcheck/00install.out:

* installing *source* package ‘iClusterPlus’ ...
 This package has only been tested with gfortran.
 So some checks are needed.
 R_HOME is /Library/Frameworks/R.framework/Resources
Attempting to determine R_ARCH...
R_ARCH is 
Attempting to detect how R was configured for Fortran 90....
  R configured for gfortran; Good!
configure: creating ./config.status
config.status: creating src/Makevars
** libs
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 iClusterPlus.c -o iClusterPlus.o
gfortran-4.2 -arch x86_64 -fdefault-real-8 -ffixed-form -fno-common -g -O2  -c  newGLMnet.f90 -o newGLMnet.o
gfortran-4.2 -arch x86_64 -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 iClusterPlus.so iClusterPlus.o newGLMnet.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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-3.0-bioc/meat/iClusterPlus.Rcheck/iClusterPlus/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iClusterPlus)

iClusterPlus.Rcheck/iClusterPlus-Ex.timings:

nameusersystemelapsed
CNregions0.0010.0000.001
compute.pod0.0010.0010.000
iCluster7.8010.0777.900
iCluster20.5830.0110.630
iClusterPlus0.0010.0000.001
plotHeatmap0.0010.0000.001
plotRI0.0010.0000.001
plotiCluster000
tune.iClusterPlus0.0000.0000.001
utility0.0000.0000.001