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BioC 3.4: CHECK report for immunoClust on zin1

This page was generated on 2016-09-21 03:39:41 -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: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings immunoClust_1.5.1.tar.gz
StartedAt: 2016-09-20 08:06:59 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:11:12 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 252.7 seconds
RetCode: 0
Status:  OK 
CheckDir: immunoClust.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings immunoClust_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/immunoClust.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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            72.892  0.048  72.951
cell.process       70.168  0.012  70.180
cell.SubClustering 23.040  0.148  23.203
* 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
  ‘/home/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/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
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_meta.cpp -o R_meta.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_model.cpp -o R_model.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c dist_mvn.cpp -o dist_mvn.o
dist_mvn.cpp: In member function ‘int dist_mvn::hellinger(double*)’:
dist_mvn.cpp:56:14: warning: variable ‘det_k’ set but not used [-Wunused-but-set-variable]
  double det, det_k, det_l, logD;
              ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function ‘double em_meta::bt_step()’:
em_meta.cpp:438:10: warning: variable ‘sndLike’ set but not used [-Wunused-but-set-variable]
   double sndLike = 0.0;
          ^
em_meta.cpp: In member function ‘int em_meta::wt_step()’:
em_meta.cpp:539:9: warning: variable ‘minNk’ set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:541:9: warning: variable ‘minDelta’ set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
em_meta.cpp: In member function ‘int em_meta::st_step()’:
em_meta.cpp:609:9: warning: variable ‘minNk’ set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:611:9: warning: variable ‘minDelta’ set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
em_meta.cpp: In member function ‘int em_meta::final(int*, double*, int*)’:
em_meta.cpp:1118:10: warning: variable ‘maxLike’ set but not used [-Wunused-but-set-variable]
   double maxLike = 0;
          ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c em_mvn.cpp -o em_mvn.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function ‘int em_mvt::t_step()’:
em_mvt.cpp:522:9: warning: variable ‘minNk’ set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hc_meta.cpp -o hc_meta.o
hc_meta.cpp: In member function ‘int mvn_dendro::mahalanobis_w(int*, int*, double*)’:
hc_meta.cpp:814:16: warning: variable ‘S_i’ set but not used [-Wunused-but-set-variable]
  const double *S_i, *S_j;
                ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hc_mvn.cpp -o hc_mvn.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c immunoClust.c -o immunoClust.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c meta_gpa.cpp -o meta_gpa.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c meta_norm.cpp -o meta_norm.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c meta_scale.cpp -o meta_scale.o
meta_scale.cpp: In member function ‘void meta_scale::quantile()’:
meta_scale.cpp:846:10: warning: variable ‘w’ set but not used [-Wunused-but-set-variable]
  double *w, *m, *s;
          ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c normalize.cpp -o normalize.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sub_mvn.cpp -o sub_mvn.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c util.cpp -o util.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c vs_htrans.cpp -o vs_htrans.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/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 -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/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.ClustData4.0240.4844.523
cell.EM2.9440.0002.944
cell.FitModel2.9760.0002.977
cell.ME2.1320.0042.134
cell.SubClustering23.040 0.14823.203
cell.hclust0.0080.0000.008
cell.process70.168 0.01270.180
cell.removed0.0160.0000.015
dat.exp1.6080.0001.615
dat.fcs72.892 0.04872.951
dat.meta0.0080.0000.006
immunoClust.object0.0040.0000.006
meta.ME0.0160.0000.019
meta.SubClustering0.1760.0000.176
meta.clustering1.8640.0001.864
meta.export1.740.001.74
meta.exprs0.0120.0000.013
meta.hclust0.0040.0000.006
meta.normalize0.0040.0000.003
meta.plot2.4400.0362.474
meta.process1.7640.0041.769
meta.regnorm0.0080.0000.006
plot.immunoClust0.5720.0040.576
splom.immunoClust0.7640.0040.783
trans.ApplyToData0.0600.0000.061
trans.FitToData0.6240.0000.636