Qianxing Mo
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/iClusterPlus |
| Branch: RELEASE_3_6 |
| Last Commit: 44b9bd3 |
| Last Changed Date: 2017-10-30 12:40:10 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:43 -0400 (Thu, 12 Apr 2018).
| Package 677/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| iClusterPlus 1.14.0 Qianxing Mo
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: iClusterPlus |
| Version: 1.14.0 |
| Command: rm -rf iClusterPlus.buildbin-libdir iClusterPlus.Rcheck && mkdir iClusterPlus.buildbin-libdir iClusterPlus.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iClusterPlus.buildbin-libdir iClusterPlus_1.14.0.tar.gz >iClusterPlus.Rcheck\00install.out 2>&1 && cp iClusterPlus.Rcheck\00install.out iClusterPlus-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iClusterPlus.buildbin-libdir --install="check:iClusterPlus-install.out" --force-multiarch --no-vignettes --timings iClusterPlus_1.14.0.tar.gz |
| StartedAt: 2018-04-12 00:47:19 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:51:54 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 275.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iClusterPlus.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf iClusterPlus.buildbin-libdir iClusterPlus.Rcheck && mkdir iClusterPlus.buildbin-libdir iClusterPlus.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=iClusterPlus.buildbin-libdir iClusterPlus_1.14.0.tar.gz >iClusterPlus.Rcheck\00install.out 2>&1 && cp iClusterPlus.Rcheck\00install.out iClusterPlus-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=iClusterPlus.buildbin-libdir --install="check:iClusterPlus-install.out" --force-multiarch --no-vignettes --timings iClusterPlus_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/iClusterPlus.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'iClusterPlus/DESCRIPTION' ... OK
* this is package 'iClusterPlus' version '1.14.0'
* 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 whether package 'iClusterPlus' can be installed ... OK
* checking installed package size ... NOTE
installed size is 23.0Mb
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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/iClusterPlus.buildbin-libdir/iClusterPlus/libs/i386/iClusterPlus.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.6-bioc/meat/iClusterPlus.Rcheck/00check.log'
for details.
iClusterPlus.Rcheck/00install.out
install for i386
* installing *source* package 'iClusterPlus' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_32/bin/gfortran -fdefault-real-8 -ffixed-form -O3 -mtune=generic -c newGLMnet.f90 -o newGLMnet.o
C:/Rtools/mingw_32/bin/gfortran -shared -s -static-libgcc -o iClusterPlus.dll tmp.def iClusterPlus.o newGLMnet.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/iClusterPlus.buildbin-libdir/iClusterPlus/libs/i386
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'iClusterPlus'
finding HTML links ... done
CNregions html
breast.chr17 html
compute.pod html
coord html
gbm html
glp html
iCluster html
iCluster2 html
iClusterPlus html
plotHeatmap html
plotRI html
plotiCluster html
simuResult html
tune.iCluster2 html
tune.iClusterPlus html
utility html
variation.hg18.v10.nov.2010 html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'iClusterPlus' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -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;
^
C:/Rtools/mingw_64/bin/gfortran -fdefault-real-8 -ffixed-form -O2 -mtune=generic -c newGLMnet.f90 -o newGLMnet.o
C:/Rtools/mingw_64/bin/gfortran -shared -s -static-libgcc -o iClusterPlus.dll tmp.def iClusterPlus.o newGLMnet.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/iClusterPlus.buildbin-libdir/iClusterPlus/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'iClusterPlus' as iClusterPlus_1.14.0.zip
* DONE (iClusterPlus)
In R CMD INSTALL
In R CMD INSTALL
|
iClusterPlus.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Thu Apr 12 00:50:19 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
98.06 0.15 98.21
|
iClusterPlus.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Thu Apr 12 00:51:49 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
89.75 0.25 90.01
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iClusterPlus.Rcheck/examples_i386/iClusterPlus-Ex.timings
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iClusterPlus.Rcheck/examples_x64/iClusterPlus-Ex.timings
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