flowPeaks 1.15.0
Yongchao Ge
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowPeaks | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ ERROR ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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###
### Running command:
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### rm -rf flowPeaks.buildbin-libdir flowPeaks.Rcheck && mkdir flowPeaks.buildbin-libdir flowPeaks.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowPeaks.buildbin-libdir flowPeaks_1.15.0.tar.gz >flowPeaks.Rcheck\00install.out 2>&1 && cp flowPeaks.Rcheck\00install.out flowPeaks-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowPeaks.buildbin-libdir --install="check:flowPeaks-install.out" --force-multiarch --no-vignettes --timings flowPeaks_1.15.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/flowPeaks.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowPeaks/DESCRIPTION' ... OK
* this is package 'flowPeaks' version '1.15.0'
* 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 'flowPeaks' can be installed ... OK
* checking installed package size ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Call with DUP:
.C("Rpack_kmeans", as.double(t(data.matrix(x))), as.integer(n),
as.integer(p), as.integer(K), cluster = integer(n), m = double(K *
p), nc = integer(K), S = double(K * p * p), Nb = integer(K *
K), twss = double(1), as.double(stime), DUP = FALSE,
PACKAGE = "flowPeaks")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
getS0K : <anonymous>: no visible global function definition for
'nclass.FD'
getS0K: no visible global function definition for 'median'
plot.flowPeaks: no visible global function definition for 'hist'
plot.flowPeaks: no visible global function definition for 'points'
plot.flowPeaks: no visible global function definition for 'plot'
plot.flowPeaks: no visible global function definition for 'text'
plot.flowPeaks: no visible global function definition for 'par'
plot.flowPeaks: no visible global function definition for 'segments'
traditional.kmeans: no visible global function definition for 'kmeans'
traditional.kmeans: no visible global function definition for 'var'
Undefined global functions or variables:
hist kmeans median nclass.FD par plot points segments text var
Consider adding
importFrom("grDevices", "nclass.FD")
importFrom("graphics", "hist", "par", "plot", "points", "segments",
"text")
importFrom("stats", "kmeans", "median", "var")
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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/flowPeaks.buildbin-libdir/flowPeaks/libs/i386/flowPeaks.dll':
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 the system RNG.
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' ... ERROR
Running examples in 'flowPeaks-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flowPeaks
> ### Title: Doing the flowPeaks analysis
> ### Aliases: flowPeaks
> ### Keywords: cluster,multivariate,smooth
>
> ### ** Examples
>
> ##demonstrate how to use a flowFrame
> ## Not run:
> ##D require(flowCore)
> ##D samp <- read.FCS(system.file("extdata","0877408774.B08",
> ##D package="flowCore"))
> ##D ##do the clustering based on the asinh transforamtion of
> ##D ##the first two FL channels
> ##D fp<-flowPeaks(asinh(samp@exprs[,3:4]))
> ##D plot(fp)
> ## End(Not run)
>
> data(barcode)
> fp<-flowPeaks(barcode[,c(1,3)])
Starting the flow Peaks analysis...
Task A: compute kmeans...
step 0, set the intial seeds, tot.wss=2.66069e+009
step 1, do the rough EM, tot.wss=1.69145e+009 at 0.339 sec
step 2, do the fine transfer of Hartigan-Wong Algorithm
tot.wss=1.69036e+009 at 0.558 sec
...finished summarization at 0.59 sec
Task B: find peaks...
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
flowPeaks 5.83 0.04 5.88
* 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: 1 ERROR, 3 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/flowPeaks.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'flowPeaks' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c Rpack.cpp -o Rpack.o
Rpack.cpp: In function 'void Rpack_relevel(int*, int*, int*, int*, int*, int*)':
Rpack.cpp:141:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(levels.size()<(i+1)){
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c Rregistrate.cpp -o Rregistrate.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c flowPeaks.cpp -o flowPeaks.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c func_collect.cpp -o func_collect.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c func_collect_supp.cpp -o func_collect_supp.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c gvector_gmatrix.cpp -o gvector_gmatrix.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c kd_tree.cpp -o kd_tree.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/i386/include -O2 -Wall -mtune=core2 -c kmns.cpp -o kmns.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowPeaks.dll tmp.def Rpack.o Rregistrate.o VoronoiDiagramGenerator.o flowPeaks.o func_collect.o func_collect_supp.o gvector_gmatrix.o kd_tree.o kmns.o -Lc:/local323/i386/lib -lgsl -lgslcblas -lm -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/flowPeaks.buildbin-libdir/flowPeaks/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'flowPeaks' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c Rpack.cpp -o Rpack.o
Rpack.cpp: In function 'void Rpack_relevel(int*, int*, int*, int*, int*, int*)':
Rpack.cpp:141:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(levels.size()<(i+1)){
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c Rregistrate.cpp -o Rregistrate.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c flowPeaks.cpp -o flowPeaks.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c func_collect.cpp -o func_collect.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c func_collect_supp.cpp -o func_collect_supp.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c gvector_gmatrix.cpp -o gvector_gmatrix.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c kd_tree.cpp -o kd_tree.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"c:/local323/include" -Ic:/local323/x64/include -O2 -Wall -mtune=core2 -c kmns.cpp -o kmns.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowPeaks.dll tmp.def Rpack.o Rregistrate.o VoronoiDiagramGenerator.o flowPeaks.o func_collect.o func_collect_supp.o gvector_gmatrix.o kd_tree.o kmns.o -Lc:/local323/x64/lib -lgsl -lgslcblas -lm -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/flowPeaks.buildbin-libdir/flowPeaks/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowPeaks' as flowPeaks_1.15.0.zip
* DONE (flowPeaks)