Back to the "Multiple platform build/check report" A  B  C  D  E [F] G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 78/264HostnameOS / ArchBUILDCHECKBUILD BIN
flowClust 1.0.0
Raphael Gottardo
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowClust
Last Changed Rev: 30947 / Revision: 30951
Last Changed Date: 2008-04-08 22:34:40 -0700 (Tue, 08 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK [ WARNINGS ]
wilson2 Linux (openSUSE 10.3) / x86_64  OK  WARNINGS 
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: flowClust
Version: 1.0.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check flowClust_1.0.0.tar.gz
StartedAt: 2008-04-09 04:38:19 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 04:40:41 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 141.8 seconds
RetCode: 0
Status: WARNINGS
CheckDir: flowClust.Rcheck
Warnings: 5

Command output

* checking for working pdflatex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/flowClust.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'flowClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowClust' version '1.0.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowClust' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:50", when none found
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:58", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:58", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:38:58", when none found
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:00", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:00", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:00", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:00", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:00", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:01", when none found
See the chapter 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:08", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:39:09", when none found
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating flowClust-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
The EM required 7 iterations
The tolerance is 3.49819e-06
The EM required 7 iterations
The tolerance is 8.62067e-06
The EM required 15 iterations
The tolerance is 7.0588e-06
The EM required 12 iterations
The tolerance is 7.93929e-06
The EM required 65 iterations
The tolerance is 9.81278e-06
The EM required 34 iterations
The tolerance is 9.85601e-06
The EM required 40 iterations
The tolerance is 9.44914e-06
The EM required 14 iterations
The tolerance is 9.97264e-06
The EM required 12 iterations
The tolerance is 7.93929e-06
The EM required 14 iterations
The tolerance is 9.97264e-06
The EM required 7 iterations
The tolerance is 3.49819e-06
The EM required 7 iterations
The tolerance is 8.62067e-06
The EM required 15 iterations
The tolerance is 7.0588e-06
The EM required 12 iterations
The tolerance is 7.93929e-06
The EM required 65 iterations
The tolerance is 9.81278e-06
The EM required 34 iterations
The tolerance is 9.85601e-06
The EM required 40 iterations
The tolerance is 9.44914e-06
The EM required 14 iterations
The tolerance is 9.97264e-06
The EM required 12 iterations
The tolerance is 7.93929e-06
The EM required 14 iterations
The tolerance is 9.97264e-06
--- running texi2dvi on vignettes
* creating flowClust-manual.tex ... OK
* checking flowClust-manual.tex using pdflatex ... OK

WARNING: There were 5 warnings, see
  /home/biocbuild/bbs-2.2-bioc/meat/flowClust.Rcheck/00check.log
for details

flowClust.Rcheck/00install.out:

* Installing *source* package 'flowClust' ...
checking for g77... g77
checking for Fortran 77 compiler default output file name... a.out
checking whether the Fortran 77 compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU Fortran 77 compiler... no
checking whether g77 accepts -g... yes
checking how to get verbose linking output from g77... -v
checking for Fortran 77 libraries of g77...  -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5 -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../lib64 -L/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c BoxCox.c -o BoxCox.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c flowClust.c -o flowClust.o
flowClust.c: In function 'up_date_z_weight':
flowClust.c:276: warning: unused variable 'row4'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ranMVNT.c -o ranMVNT.o
ranMVNT.c: In function 'gsl_mahalanobis':
ranMVNT.c:170: warning: 'PrecisionTmp' may be used uninitialized in this function
ranMVNT.c: In function 'gsl_ran_mvngaussian':
ranMVNT.c:110: warning: 'PrecisionTmp' may be used uninitialized in this function
ranMVNT.c: In function 'gsl_ran_mvnt':
ranMVNT.c:139: warning: 'PrecisionTmp' may be used uninitialized in this function
ranMVNT.c: In function 'gsl_ran_mvnt_pdf':
ranMVNT.c:60: warning: 'PrecisionTmp' may be used uninitialized in this function
ranMVNT.c: In function 'gsl_ran_mvngaussian_pdf':
ranMVNT.c:7: warning: 'PrecisionTmp' may be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib64 -o flowClust.so BoxCox.o flowClust.o ranMVNT.o -lgslcblas -lgsl  -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: mnormt
Loading required package: mclust
use of mclust requires a license agreement
see http://www.stat.washington.edu/mclust/license.txt
Loading required package: ellipse
Loading required package: flowCore
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: rrcov
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 0.4-05)

Attaching package: 'rrcov'


	The following object(s) are masked from package:stats :

	 biplot,
	 predict,
	 screeplot 

Loading required package: feature
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: misc3d
Loading required package: rgl

Attaching package: 'flowCore'


	The following object(s) are masked from package:Biobase :

	 description 


	The following object(s) are masked from package:stats :

	 filter 

** help
 >>> Building/Updating help pages for package 'flowClust'
     Formats: text html latex example 
  Map                               text    html    latex   example
  SimulateMixture                   text    html    latex   example
  Subset                            text    html    latex
  box                               text    html    latex   example
  density                           text    html    latex   example
  dmvt                              text    html    latex
  flowClust-internal                text    html    latex
  flowClust-package                 text    html    latex
  flowClust                         text    html    latex   example
  hist                              text    html    latex   example
  plot.flowClust                    text    html    latex   example
  plot.flowCore                     text    html    latex
  plot.flowDens                     text    html    latex
  posterior                         text    html    latex   example
  rbox                              text    html    latex
  rituximab                         text    html    latex
  ruleOutliers                      text    html    latex   example
  show.flowClust                    text    html    latex
  show.tmixFilter                   text    html    latex
  split                             text    html    latex
  summary                           text    html    latex
  tmixFilter                        text    html    latex   example
** building package indices ...
* DONE (flowClust)