BioC 3.4: CHECK report for iClusterPlus on zin1

Package: iClusterPlus

Version: 1.9.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iClusterPlus_1.9.0.tar.gz

StartedAt: 2016-09-20 08:00:19 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:03:49 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 210.7 seconds

RetCode: 0

Status:  OK

CheckDir: iClusterPlus.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings iClusterPlus_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/iClusterPlus.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 ‘iClusterPlus/DESCRIPTION’ ... OK
* this is package ‘iClusterPlus’ version ‘1.9.0’
* 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 ... 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: no visible global function definition for ‘tail’
CNregions: no visible global function definition for ‘quantile’
CNregions : get.medoid: no visible global function definition for ‘pam’
classError: no visible global function definition for ‘mapClass’
compute.pod: no visible global function definition for ‘model.matrix’
iCluster: no visible global function definition for ‘kmeans’
iCluster2: no visible global function definition for ‘kmeans’
iClusterPlus: no visible global function definition for ‘rnorm’
iClusterPlus: no visible global function definition for ‘kmeans’
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: no visible global function definition for ‘quantile’
plotHeatmap: no visible global function definition for ‘cor’
plotHeatmap: no visible global function definition for ‘hclust’
plotHeatmap: no visible global function definition for ‘as.dist’
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 : scale.fn: no visible binding for global variable ‘sd’
plotHeatmap: no visible global function definition for ‘levelplot’
plotRI: no visible global function definition for ‘plot’
plotRI: no visible global function definition for ‘axis’
plotiCluster: no visible global function definition for ‘image’
plotiCluster: no visible global function definition for ‘gray’
plotiCluster: no visible global function definition for ‘axis’
plotiCluster: no visible global function definition for ‘mtext’
plotiCluster: no visible global function definition for ‘box’
predict.kmeans: no visible global function definition for ‘dist’
tune.iCluster2: no visible global function definition for ‘data’
tune.iCluster2: no visible binding for global variable ‘glp’
tune.iClusterPlus: no visible global function definition for ‘data’
tune.iClusterPlus: no visible binding for global variable ‘glp’
tune.iClusterPlus: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  GRanges IRanges as.dist axis bluered box chromosome cor data dist
  findOverlaps glp gray hclust image kmeans levelplot mapClass mclapply
  model.matrix mtext num.mark pam panel.abline panel.levelplot plot
  quantile rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "box", "image", "mtext", "plot")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "kmeans",
             "model.matrix", "quantile", "rnorm", "sd")
  importFrom("utils", "data", "tail")
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 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.4-bioc/meat/iClusterPlus.Rcheck/00check.log’
for details.

* installing *source* package ‘iClusterPlus’ ...
 This package has only been tested with gfortran.
 So some checks are needed.
 R_HOME is /home/biocbuild/bbs-3.4-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 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c iClusterPlus.c -o iClusterPlus.o
iClusterPlus.c: In function ‘iClusterCore’:
iClusterPlus.c:1098:60: warning: unused variable ‘tempm3’ [-Wunused-variable]
   double *btp,*btpb, *EXZt,*tempX,*tempm0,*tempm1,*tempm2,*tempm3,*BOld,*PhivecOld, *XtXdiag;
                                                            ^
iClusterPlus.c:1096:18: warning: variable ‘pp’ set but not used [-Wunused-but-set-variable]
   int i, j,kk,pk,pp,s,t;
                  ^
gfortran -fdefault-real-8 -ffixed-form -fpic -g -O2  -c  newGLMnet.f90 -o newGLMnet.o
gfortran -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o iClusterPlus.so iClusterPlus.o newGLMnet.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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)

name	user	system	elapsed
CNregions	0.000	0.000	0.001
compute.pod	0.000	0.000	0.001
iCluster	4.264	0.024	4.288
iCluster2	0.384	0.004	0.390
iClusterPlus	0	0	0
plotHeatmap	0	0	0
plotRI	0.000	0.000	0.001
plotiCluster	0.000	0.000	0.001
tune.iClusterPlus	0	0	0
utility	0	0	0