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BioC 3.2: CHECK report for iClusterPlus on linux1.bioconductor.org

This page was generated on 2015-10-27 17:26:16 -0400 (Tue, 27 Oct 2015).

Package 516/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iClusterPlus 1.6.0
Qianxing Mo , Ronglai Shen
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/iClusterPlus
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: iClusterPlus
Version: 1.6.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings iClusterPlus_1.6.0.tar.gz
StartedAt: 2015-10-27 04:45:26 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:47:34 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 128.4 seconds
RetCode: 0
Status:  OK 
CheckDir: iClusterPlus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings iClusterPlus_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/iClusterPlus.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iClusterPlus/DESCRIPTION’ ... OK
* this is package ‘iClusterPlus’ version ‘1.6.0’
* 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 ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is 22.7Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
    doc    3.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
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’
classError: no visible global function definition for ‘mapClass’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
iCluster 7.249  0.048   7.296
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [85s/85s]
 [85s/85s] 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
  ‘/home/biocbuild/bbs-3.2-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 /home/biocbuild/bbs-3.2-bioc/R
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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c iClusterPlus.c -o iClusterPlus.o
gfortran -fdefault-real-8 -ffixed-form -fpic -g -O2  -c  newGLMnet.f90 -o newGLMnet.o
gfortran -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o iClusterPlus.so iClusterPlus.o newGLMnet.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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
CNregions0.0010.0000.000
compute.pod0.0000.0000.001
iCluster7.2490.0487.296
iCluster20.8110.0000.811
iClusterPlus000
plotHeatmap000
plotRI000
plotiCluster000
tune.iClusterPlus000
utility000