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BioC 3.4: CHECK report for immunoClust on morelia

This page was generated on 2016-09-21 03:54:12 -0700 (Wed, 21 Sep 2016).

Package 611/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunoClust 1.5.1
Till Soerensen
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/immunoClust
Last Changed Rev: 119423 / Revision: 121152
Last Changed Date: 2016-07-18 00:56:30 -0700 (Mon, 18 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: immunoClust
Version: 1.5.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings immunoClust_1.5.1.tar.gz
StartedAt: 2016-09-20 08:06:17 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:09:45 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 207.8 seconds
RetCode: 0
Status:  OK 
CheckDir: immunoClust.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings immunoClust_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/immunoClust.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘immunoClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunoClust’ version ‘1.5.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘immunoClust’ can be installed ... OK
* checking installed package size ... OK
* 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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
meta.plotExpClusters: no visible global function definition for ‘png’
meta.plotExpClusters: no visible global function definition for
  ‘dev.off’
meta.plotExpResult: no visible global function definition for ‘png’
meta.plotExpResult: no visible global function definition for ‘dev.off’
meta.plotGate: no visible global function definition for ‘png’
meta.plotGate: no visible global function definition for ‘dev.off’
meta.plotGating: no visible global function definition for ‘png’
meta.plotGating: no visible global function definition for ‘dev.off’
plot,immunoClust-missing: no visible global function definition for
  ‘title’
Undefined global functions or variables:
  dev.off png title
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "title")
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
dat.fcs            66.918  0.305  67.279
cell.process       65.782  0.207  65.994
cell.SubClustering  9.657  0.066   9.723
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/immunoClust.Rcheck/00check.log’
for details.


immunoClust.Rcheck/00install.out:

* installing *source* package ‘immunoClust’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_meta.cpp -o R_meta.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_model.cpp -o R_model.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c dist_mvn.cpp -o dist_mvn.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c em_meta.cpp -o em_meta.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c em_mvn.cpp -o em_mvn.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c em_mvt.cpp -o em_mvt.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hc_meta.cpp -o hc_meta.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hc_mvn.cpp -o hc_mvn.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c immunoClust.c -o immunoClust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c meta_gpa.cpp -o meta_gpa.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c meta_norm.cpp -o meta_norm.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c meta_scale.cpp -o meta_scale.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c normalize.cpp -o normalize.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sub_mvn.cpp -o sub_mvn.o
In file included from sub_mvn.cpp:10:
./sub_mvn.h:21:16: warning: private field 'W' is not used [-Wunused-private-field]
        const double* W;
                      ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c util.cpp -o util.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c vs_htrans.cpp -o vs_htrans.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o immunoClust.so R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o hc_meta.o hc_mvn.o immunoClust.o meta_gpa.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/immunoClust.Rcheck/immunoClust/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘splom’ from package ‘lattice’ in package ‘immunoClust’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (immunoClust)

immunoClust.Rcheck/immunoClust-Ex.timings:

nameusersystemelapsed
cell.ClustData1.4140.0101.423
cell.EM0.8130.0080.821
cell.FitModel0.8600.0040.863
cell.ME0.5730.0030.577
cell.SubClustering9.6570.0669.723
cell.hclust0.0070.0010.007
cell.process65.782 0.20765.994
cell.removed0.0120.0030.015
dat.exp0.8340.0060.840
dat.fcs66.918 0.30567.279
dat.meta0.0050.0010.006
immunoClust.object0.0060.0010.007
meta.ME0.0180.0030.020
meta.SubClustering0.0960.0010.098
meta.clustering0.9080.0030.911
meta.export0.8850.0040.888
meta.exprs0.0110.0010.012
meta.hclust0.0050.0000.005
meta.normalize0.0020.0010.004
meta.plot1.9880.0432.059
meta.process0.8720.0080.880
meta.regnorm0.0050.0010.005
plot.immunoClust0.5780.0120.610
splom.immunoClust0.6260.0070.649
trans.ApplyToData0.0450.0010.046
trans.FitToData0.2500.0070.257