flowClust 3.11.1
Greg Finak , Mike Jiang
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust | | Last Changed Rev: 118918 / Revision: 121152 | | Last Changed Date: 2016-06-23 16:23:33 -0700 (Thu, 23 Jun 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:
###
### rm -rf flowClust.buildbin-libdir flowClust.Rcheck && mkdir flowClust.buildbin-libdir flowClust.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowClust.buildbin-libdir flowClust_3.11.1.tar.gz >flowClust.Rcheck\00install.out 2>&1 && cp flowClust.Rcheck\00install.out flowClust-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowClust.buildbin-libdir --install="check:flowClust-install.out" --force-multiarch --no-vignettes --timings flowClust_3.11.1.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/flowClust.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 'flowClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowClust' version '3.11.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase' 'graph' 'RBGL' 'ellipse' 'flowViz' 'mnormt' 'corpcor'
'flowCore' 'clue'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'flowClust' 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 ... NOTE
'library' or 'require' call to 'parallel' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'RBGL' 'corpcor' 'ellipse' 'flowViz' 'mnormt'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'flowViz:::fplot'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.estimateHyperParameters: no visible global function definition for
'cov.shrink'
.estimateHyperParameters: no visible global function definition for
'cov'
.estimateHyperParameters: no visible binding for global variable 'var'
.estimateHyperParameters: no visible global function definition for
'optimize'
.fcbMap: no visible global function definition for 'qf'
.flowClustK: no visible global function definition for 'var'
.flowClustK: no visible global function definition for 'qf'
.flowClustK: no visible global function definition for 'qchisq'
.flowClustK: no visible global function definition for 'quantile'
.flowClustK: no visible global function definition for 'kmeans'
.mergePriors: no visible global function definition for 'optim'
SimulateMixture: no visible global function definition for 'rmt'
dmvt: no visible global function definition for 'mahalanobis'
flowClust: no visible global function definition for 'detectCores'
flowClust: no visible global function definition for 'mclapply'
flowClust2Prior: no visible global function definition for 'cov'
peakMatch : <anonymous>: no visible global function definition for
'dist'
plotPrior: no visible global function definition for 'na.omit'
plotPrior: no visible global function definition for 'points'
plotPrior: no visible global function definition for 'lines'
plotPrior: no visible global function definition for 'ellipse'
plotPrior: no visible global function definition for 'abline'
plotPrior: no visible global function definition for 'qnorm'
%in%,flowFrame-tmixFilter: no visible global function definition for
'parameters'
hist,flowClust: no visible global function definition for 'curve'
hist,flowClust: no visible global function definition for 'stripchart'
mkPrior,missing-flowFrame-missing-missing: no visible global function
definition for 'cov.shrink'
mkPrior,missing-flowFrame-missing-missing: no visible global function
definition for 'cov'
mkPrior,polygonGate-flowFrame-missing-missing: no visible global
function definition for 'na.omit'
mkPrior,polygonGate-flowFrame-missing-missing: no visible global
function definition for 'parameters'
mkPrior,polygonGate-flowFrame-missing-missing: no visible global
function definition for 'cov'
mkPrior,polygonGate-flowFrame-numeric-matrix: no visible global
function definition for 'na.omit'
mkPrior,polygonGate-flowFrame-numeric-matrix: no visible global
function definition for 'parameters'
mkPrior,polygonGate-flowFrame-numeric-matrix: no visible global
function definition for 'cov'
mkPrior,rectangleGate-flowFrame-missing-missing: no visible global
function definition for 'na.omit'
mkPrior,rectangleGate-flowFrame-missing-missing: no visible global
function definition for 'parameters'
mkPrior,rectangleGate-flowFrame-missing-missing: no visible global
function definition for 'cov'
mkPrior,rectangleGate-flowFrame-numeric-matrix: no visible global
function definition for 'na.omit'
mkPrior,rectangleGate-flowFrame-numeric-matrix: no visible global
function definition for 'parameters'
mkPrior,rectangleGate-flowFrame-numeric-matrix: no visible global
function definition for 'cov'
plot,flowClust-missing: no visible global function definition for
'gray'
plot,flowClust-missing: no visible global function definition for
'title'
plot,flowClust-missing: no visible global function definition for
'points'
plot,flowClust-missing: no visible global function definition for 'qf'
plot,flowClust-missing: no visible global function definition for
'qchisq'
plot,flowClustList-missing: no visible global function definition for
'gray'
plot,flowDens-missing: no visible global function definition for
'contour'
plot,flowDens-missing: no visible global function definition for
'heat.colors'
plot,flowDens-missing: no visible global function definition for
'rainbow'
plot,flowDens-missing: no visible global function definition for
'terrain.colors'
plot,flowDens-missing: no visible global function definition for
'topo.colors'
plot,flowDens-missing: no visible global function definition for
'cm.colors'
plot,flowDens-missing: no visible global function definition for 'gray'
plot,flowDens-missing: no visible global function definition for
'image'
ruleOutliers<-,flowClust-list: no visible global function definition
for 'qf'
ruleOutliers<-,flowClust-list: no visible global function definition
for 'qchisq'
show,tmixFilter: no visible global function definition for 'parameters'
summarizeFilter,tmixFilterResult-tmixFilter: no visible global function
definition for 'parameters'
Undefined global functions or variables:
abline cm.colors contour cov cov.shrink curve detectCores dist
ellipse gray heat.colors image kmeans lines mahalanobis mclapply
na.omit optim optimize parameters points qchisq qf qnorm quantile
rainbow rmt stripchart terrain.colors title topo.colors var
Consider adding
importFrom("grDevices", "cm.colors", "gray", "heat.colors", "rainbow",
"terrain.colors", "topo.colors")
importFrom("graphics", "abline", "contour", "curve", "image", "lines",
"points", "stripchart", "title")
importFrom("stats", "cov", "dist", "kmeans", "mahalanobis", "na.omit",
"optim", "optimize", "qchisq", "qf", "qnorm", "quantile",
"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 ... NOTE
GNU make is a SystemRequirements.
* 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/flowClust.buildbin-libdir/flowClust/libs/i386/flowClust.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 'flowClust-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flowClust
> ### Title: Robust Model-based Clustering for Flow Cytometry
> ### Aliases: flowClust flowClust-class flowClustList flowClustList-class
> ### %in%,ANY,flowClust-method %in%,ANY,flowClustList-method
> ### [,flowFrame,flowClust-method [,flowFrame,flowClustList-method
> ### [,flowFrame,flowClust,ANY,ANY-method
> ### [,flowFrame,flowClustList,ANY,ANY-method
> ### Keywords: cluster models
>
> ### ** Examples
>
> data(rituximab)
>
> ### cluster the data using FSC.H and SSC.H
> res1 <- flowClust(rituximab, varNames=c("FSC.H", "SSC.H"), K=1)
Using the parallel (multicore) version of flowClust with 16 cores
** 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: 1 ERROR, 5 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/flowClust.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'flowClust' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/i386/include -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c BoxCox.c -o BoxCox.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/i386/include -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
rowPrecision, rowZ, rowLambda0;
^
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
double *nu0 = p->nu0, kappa0 = p->kappa0;
^
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
int *itersolve = p->itersolve;
^
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
int iter = p->iter;
^
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
int model = *p->model;
^
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
gsl_vector *SumZlogY = p->SumZlogY;
^
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
gsl_matrix *Precision = p->Precision; // will be updated
^
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/i386/include -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Nu.c -o Nu.o
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/i386/include -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
matrixZUY2;
^
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
int i=0;
^
flowClust.c: In function 'flowClust':
flowClust.c:383:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^
flowClust.c:713:12: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
nu_hi = gsl_min_fminimizer_x_upper(s3);
^
flowClust.c:675:14: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
nu_hi = gsl_root_fsolver_x_upper(s2);
^
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/i386/include -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:242:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^
C:/Rtools/mingw_32/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/i386/include -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ranMVNT.c -o ranMVNT.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.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/flowClust.buildbin-libdir/flowClust/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 'flowClust' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/x64/include -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c BoxCox.c -o BoxCox.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/x64/include -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function 'BoxCoxGradientPriors':
BoxCoxPriors.c:57:16: warning: unused variable 'rowZ' [-Wunused-variable]
rowPrecision, rowZ, rowLambda0;
^
BoxCoxPriors.c:33:24: warning: unused variable 'kappa0' [-Wunused-variable]
double *nu0 = p->nu0, kappa0 = p->kappa0;
^
BoxCoxPriors.c:32:7: warning: unused variable 'itersolve' [-Wunused-variable]
int *itersolve = p->itersolve;
^
BoxCoxPriors.c:31:6: warning: unused variable 'iter' [-Wunused-variable]
int iter = p->iter;
^
BoxCoxPriors.c:28:6: warning: unused variable 'model' [-Wunused-variable]
int model = *p->model;
^
BoxCoxPriors.c:23:14: warning: unused variable 'SumZlogY' [-Wunused-variable]
gsl_vector *SumZlogY = p->SumZlogY;
^
BoxCoxPriors.c:15:14: warning: unused variable 'Precision' [-Wunused-variable]
gsl_matrix *Precision = p->Precision; // will be updated
^
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/x64/include -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Nu.c -o Nu.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/x64/include -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c flowClust.c -o flowClust.o
flowClust.c: In function 'flowClust':
flowClust.c:48:2: warning: unused variable 'matrixZUY2' [-Wunused-variable]
matrixZUY2;
^
flowClust.c:46:48: warning: unused variable 'subRowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^
flowClust.c:46:39: warning: unused variable 'rowZUY2' [-Wunused-variable]
rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
^
flowClust.c: In function 'ECMUpdateSigmaG2':
flowClust.c:1111:6: warning: unused variable 'i' [-Wunused-variable]
int i=0;
^
flowClust.c: In function 'flowClust':
flowClust.c:383:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^
flowClust.c:713:12: warning: 's3' may be used uninitialized in this function [-Wmaybe-uninitialized]
nu_hi = gsl_min_fminimizer_x_upper(s3);
^
flowClust.c:675:14: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized]
nu_hi = gsl_root_fsolver_x_upper(s2);
^
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/x64/include -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function 'flowClustGaussian':
flowClustGaussian.c:242:13: warning: 's' may be used uninitialized in this function [-Wmaybe-uninitialized]
x_hi = gsl_root_fsolver_x_upper(s);
^
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I/src/include -Ic:/local323/x64/include -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ranMVNT.c -o ranMVNT.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o flowClust.dll tmp.def BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.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/flowClust.buildbin-libdir/flowClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowClust' as flowClust_3.11.1.zip
* DONE (flowClust)