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CHECK report for iClusterPlus on malbec2

This page was generated on 2018-10-17 08:25:47 -0400 (Wed, 17 Oct 2018).

Package 712/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iClusterPlus 1.16.0
Qianxing Mo , Ronglai Shen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/iClusterPlus
Branch: RELEASE_3_7
Last Commit: 6db4562
Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: iClusterPlus
Version: 1.16.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:iClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings iClusterPlus_1.16.0.tar.gz
StartedAt: 2018-10-16 01:13:13 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:14:42 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 89.1 seconds
RetCode: 0
Status:  OK 
CheckDir: iClusterPlus.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:iClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings iClusterPlus_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/iClusterPlus.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.16.0’
* 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 ... 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 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’
iClusterBayes: no visible global function definition for ‘kmeans’
iClusterPlus: no visible global function definition for ‘rnorm’
iClusterPlus: no visible global function definition for ‘kmeans’
mcmcBayes: no visible global function definition for ‘rnorm’
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: no visible global function definition for ‘cor’
plotHMBayes: no visible global function definition for ‘hclust’
plotHMBayes: no visible global function definition for ‘as.dist’
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 : scale.fn: no visible binding for global variable ‘sd’
plotHMBayes: no visible global function definition for ‘quantile’
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: 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.iClusterBayes: no visible global function definition for
  ‘mclapply’
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 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
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/iClusterPlus.Rcheck/00check.log’
for details.



Installation output

iClusterPlus.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL iClusterPlus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-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-3.7-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-3.7-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-3.7-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-3.7-bioc/R/lib -L/usr/local/lib -o iClusterPlus.so iClusterBayes.o iClusterPlus.o newGLMnet.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-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)

Tests output

iClusterPlus.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 16 01:14:39 2018 
*********************************************** 
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 
 59.256   0.136  59.479 

Example timings

iClusterPlus.Rcheck/iClusterPlus-Ex.timings

nameusersystemelapsed
CNregions0.0000.0000.001
compute.pod0.0040.0000.001
iCluster3.6320.0523.687
iCluster20.3360.0040.338
iClusterBayes000
iClusterPlus000
plotHMBayes000
plotHeatmap0.0000.0000.001
plotRI000
plotiCluster0.0040.0000.000
tune.iClusterBayes0.0000.0000.001
tune.iClusterPlus0.0000.0000.001
utility0.0000.0000.001