Yongchao Ge
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/flowPeaks |
| Branch: RELEASE_3_6 |
| Last Commit: a39749e |
| Last Changed Date: 2017-10-30 12:39:43 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:21:50 -0400 (Thu, 12 Apr 2018).
| Package 486/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowPeaks 1.22.0 Yongchao Ge
| 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 | OK | OK | |
| Package: flowPeaks |
| Version: 1.22.0 |
| Command: rm -rf flowPeaks.buildbin-libdir flowPeaks.Rcheck && mkdir flowPeaks.buildbin-libdir flowPeaks.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowPeaks.buildbin-libdir flowPeaks_1.22.0.tar.gz >flowPeaks.Rcheck\00install.out 2>&1 && cp flowPeaks.Rcheck\00install.out flowPeaks-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowPeaks.buildbin-libdir --install="check:flowPeaks-install.out" --force-multiarch --no-vignettes --timings flowPeaks_1.22.0.tar.gz |
| StartedAt: 2018-04-12 00:01:41 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:02:49 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 68.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowPeaks.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf flowPeaks.buildbin-libdir flowPeaks.Rcheck && mkdir flowPeaks.buildbin-libdir flowPeaks.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowPeaks.buildbin-libdir flowPeaks_1.22.0.tar.gz >flowPeaks.Rcheck\00install.out 2>&1 && cp flowPeaks.Rcheck\00install.out flowPeaks-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowPeaks.buildbin-libdir --install="check:flowPeaks-install.out" --force-multiarch --no-vignettes --timings flowPeaks_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowPeaks.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 'flowPeaks/DESCRIPTION' ... OK
* this is package 'flowPeaks' version '1.22.0'
* 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 'C:/Users/biocbuild/bbs-3.6-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 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
Examples with CPU or elapsed time > 5s
user system elapsed
flowPeaks 5.01 0.05 5.06
** running examples for arch 'x64' ... 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
'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowPeaks.Rcheck/00check.log'
for details.
flowPeaks.Rcheck/00install.out
install for i386
* installing *source* package 'flowPeaks' ...
** libs
rm -f flowPeaks.dll Rpack.o Rregistrate.o VoronoiDiagramGenerator.o flowPeaks.o func_collect.o func_collect_supp.o gvector_gmatrix.o kd_tree.o kmns.o
"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386/Rscript.exe" "../tools/winlibs.R"
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c Rregistrate.cpp -o Rregistrate.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c flowPeaks.cpp -o flowPeaks.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c func_collect.cpp -o func_collect.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c func_collect_supp.cpp -o func_collect_supp.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c gvector_gmatrix.cpp -o gvector_gmatrix.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c kd_tree.cpp -o kd_tree.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -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 -L../windows/gsl-master/lib-4.9.3/i386 -lgsl -lgslcblas -lm -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/flowPeaks.buildbin-libdir/flowPeaks/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'flowPeaks'
finding HTML links ... done
adjust.flowPeaks html
assign.flowPeaks html
barcode html
concave html
evalCluster html
flowPeaks html
plot.flowPeaks html
print.flowPeaks html
summary.flowPeaks html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'flowPeaks' ...
** libs
rm -f flowPeaks.dll Rpack.o Rregistrate.o VoronoiDiagramGenerator.o flowPeaks.o func_collect.o func_collect_supp.o gvector_gmatrix.o kd_tree.o kmns.o
"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64/Rscript.exe" "../tools/winlibs.R"
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -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"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c Rregistrate.cpp -o Rregistrate.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c VoronoiDiagramGenerator.cpp -o VoronoiDiagramGenerator.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c flowPeaks.cpp -o flowPeaks.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c func_collect.cpp -o func_collect.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c func_collect_supp.cpp -o func_collect_supp.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c gvector_gmatrix.cpp -o gvector_gmatrix.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -c kd_tree.cpp -o kd_tree.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I/src/include -I../windows/gsl-master/include/gsl -O2 -Wall -mtune=generic -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 -L../windows/gsl-master/lib-4.9.3/x64 -lgsl -lgslcblas -lm -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/flowPeaks.buildbin-libdir/flowPeaks/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowPeaks' as flowPeaks_1.22.0.zip
* DONE (flowPeaks)
In R CMD INSTALL
In R CMD INSTALL
|
flowPeaks.Rcheck/examples_i386/flowPeaks-Ex.timings
|
flowPeaks.Rcheck/examples_x64/flowPeaks-Ex.timings
|