Package: iClusterPlus

Version: 1.18.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:iClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings iClusterPlus_1.18.0.tar.gz

StartedAt: 2019-04-16 00:43:53 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:46:05 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 132.0 seconds

RetCode: 0

Status:  OK

CheckDir: iClusterPlus.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:iClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings iClusterPlus_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/iClusterPlus.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.18.0’
* 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 23.2Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
    doc    4.2Mb
* 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 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
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’
plotHMBayes: no visible global function definition for ‘bluered’
plotHMBayes : my.panel.levelplot: no visible global function definition
  for ‘panel.levelplot’
plotHMBayes : my.panel.levelplot: no visible global function definition
  for ‘panel.abline’
plotHMBayes : my.panel.levelplot.2: no visible global function
  definition for ‘panel.levelplot’
plotHMBayes : my.panel.levelplot.2: no visible global function
  definition for ‘panel.abline’
plotHMBayes: no visible global function definition for ‘levelplot’
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’
Undefined global functions or variables:
  GRanges IRanges bluered chromosome findOverlaps glp levelplot
  mapClass num.mark pam panel.abline panel.levelplot
* 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 shell scripts ... 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 ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
iCluster 5.636   0.08   5.731
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/iClusterPlus.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL iClusterPlus
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘iClusterPlus’ ...
 This package has only been tested with gfortran.
 So some checks are needed.
 R_HOME is /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c iClusterBayes.c -o iClusterBayes.o
iClusterBayes.c: In function ‘bvsPoisson’:
iClusterBayes.c:380:27: warning: variable ‘k1k1’ set but not used [-Wunused-but-set-variable]
   int *gamma_p,i,j,nk1,k1,k1k1,incx,incy,ID,np;
                           ^
iClusterBayes.c: In function ‘bvsBinom’:
iClusterBayes.c:629:27: warning: variable ‘k1k1’ set but not used [-Wunused-but-set-variable]
   int *gamma_p,i,j,nk1,k1,k1k1,incx,incy,ID,np;
                           ^
iClusterBayes.c: In function ‘mcmcBayes’:
iClusterBayes.c:1214:28: warning: variable ‘Zdraw’ set but not used [-Wunused-but-set-variable]
   int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k;
                            ^
iClusterBayes.c:1214:20: warning: variable ‘Zburnin’ set but not used [-Wunused-but-set-variable]
   int i,j,h,n,k,ID,Zburnin,Zdraw,ndt,nk,thin,nthin,remainder,ty0,p0,ty1,p1,ty2,p2,ty3,p3,ty4,p4,ty5,p5,betaBurnin,betaDraw,p0k,p1k,p2k,p3k,p4k,p5k;
                    ^
iClusterBayes.c:1216:174: warning: ‘gb3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
                                                                                                                                                                              ^
iClusterBayes.c:1477:5: warning: ‘gb2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
     ^
iClusterBayes.c:1477:5: warning: ‘gb1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iClusterBayes.c:1477:5: warning: ‘gb0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iClusterBayes.c:1216:179: warning: ‘gb4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
                                                                                                                                                                                   ^
iClusterBayes.c:1216:184: warning: ‘gb5’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   double *sumMeanZ,*suma0,*sumb0,*suma1,*sumb1,*suma2,*sumb2,*suma3,*sumb3,*suma4,*sumb4,*suma5,*sumb5,*sumsig0,*sumsig1,*sumsig2,*sumsig3,*sumsig4,*sumsig5,*gb0,*gb1,*gb2,*gb3,*gb4,*gb5;
                                                                                                                                                                                        ^
gcc -I"/home/biocbuild/bbs-3.8-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:1101:60: warning: unused variable ‘tempm3’ [-Wunused-variable]
   double *btp,*btpb, *EXZt,*tempX,*tempm0,*tempm1,*tempm2,*tempm3,*BOld,*PhivecOld, *XtXdiag;
                                                            ^
iClusterPlus.c:1099:18: 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-3.8-bioc/R/lib -L/usr/local/lib -o iClusterPlus.so iClusterBayes.o iClusterPlus.o newGLMnet.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.8-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/iClusterPlus/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘iClusterPlus.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (iClusterPlus)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("iClusterPlus")


RUNIT TEST PROTOCOL -- Tue Apr 16 00:46:01 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
iClusterPlus RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
 95.056   0.120  95.736 

name	user	system	elapsed
CNregions	0	0	0
compute.pod	0	0	0
iCluster	5.636	0.080	5.731
iCluster2	0.540	0.004	0.544
iClusterBayes	0	0	0
iClusterPlus	0	0	0
plotHMBayes	0.000	0.000	0.001
plotHeatmap	0	0	0
plotRI	0	0	0
plotiCluster	0	0	0
tune.iClusterBayes	0.000	0.000	0.001
tune.iClusterPlus	0	0	0
utility	0	0	0