Qianxing Mo
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/iClusterPlus |
| Branch: master |
| Last Commit: 55e0773 |
| Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:37:21 -0400 (Tue, 09 Apr 2019).
| Package 777/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iClusterPlus 1.19.0 Qianxing Mo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: iClusterPlus |
| Version: 1.19.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:iClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iClusterPlus_1.19.0.tar.gz |
| StartedAt: 2019-04-09 01:18:31 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:20:39 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 127.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iClusterPlus.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:iClusterPlus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iClusterPlus_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/iClusterPlus.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.19.0’
* 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 ... NOTE
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
* 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
* 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-3.9-bioc/meat/iClusterPlus.Rcheck/00check.log’
for details.
iClusterPlus.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL iClusterPlus
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘iClusterPlus’ ...
** using staged installation
This package has only been tested with gfortran.
So some checks are needed.
R_HOME is /home/biocbuild/bbs-3.9-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-3.9-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:1216:179: 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:1216:174: 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:1370:6: warning: ‘gb2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
mcmcMix6d(meanZ,lastZ,nkZbd,sdev,
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
&ty0,&p0,a0,gb0,con0,cat0,sigma0,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
&ty1,&p1,a1,gb1,con1,cat1,sigma1,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
&ty2,&p2,a2,gb2,con2,cat2,sigma2,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
&ty3,&p3,a3,gb3,con3,cat3,sigma3,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
&ty4,&p4,a4,gb4,con4,cat4,sigma4,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
&ty5,&p5,a5,gb5,con5,cat5,sigma5,acceptZ);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
iClusterBayes.c:1370:6: warning: ‘gb1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iClusterBayes.c:1370:6: warning: ‘gb0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
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-3.9-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
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o iClusterPlus.so iClusterBayes.o iClusterPlus.o newGLMnet.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-iClusterPlus/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iClusterPlus)
iClusterPlus.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 9 01:20:35 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
86.575 0.114 87.197
iClusterPlus.Rcheck/iClusterPlus-Ex.timings
| name | user | system | elapsed | |
| CNregions | 0 | 0 | 0 | |
| compute.pod | 0.001 | 0.001 | 0.000 | |
| iCluster | 4.195 | 0.059 | 4.256 | |
| iCluster2 | 0.371 | 0.004 | 0.375 | |
| iClusterBayes | 0 | 0 | 0 | |
| iClusterPlus | 0.000 | 0.001 | 0.000 | |
| plotHMBayes | 0 | 0 | 0 | |
| plotHeatmap | 0.000 | 0.001 | 0.000 | |
| plotRI | 0 | 0 | 0 | |
| plotiCluster | 0.000 | 0.001 | 0.000 | |
| tune.iClusterBayes | 0 | 0 | 0 | |
| tune.iClusterPlus | 0.000 | 0.001 | 0.000 | |
| utility | 0 | 0 | 0 | |