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BioC 3.4: CHECK report for COMPASS on zin1

This page was generated on 2016-09-21 03:38:47 -0700 (Wed, 21 Sep 2016).

Package 241/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.11.7
Greg Finak
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS
Last Changed Rev: 120668 / Revision: 121152
Last Changed Date: 2016-09-01 15:18:20 -0700 (Thu, 01 Sep 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: COMPASS
Version: 1.11.7
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings COMPASS_1.11.7.tar.gz
StartedAt: 2016-09-20 04:54:14 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:55:28 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 74.0 seconds
RetCode: 0
Status:  OK 
CheckDir: COMPASS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings COMPASS_1.11.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/COMPASS.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 ‘COMPASS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COMPASS’ version ‘1.11.7’
* 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 ‘COMPASS’ 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
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘flowWorkspace:::.getNodeInd’
  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
.COMPASS.discrete: no visible global function definition for ‘median’
.MakeComparableTwoCOMPASSResults : .consolidateColumns : <anonymous>:
  no visible global function definition for ‘na.omit’
.polarLegend: no visible global function definition for ‘head’
.polarLegend: no visible global function definition for ‘colorRamp’
.polarLegend: no visible global function definition for ‘rgb’
.polarLegend: no visible global function definition for ‘rgb2hsv’
.polarLegend: no visible global function definition for ‘hsv’
COMPASS: no visible global function definition for ‘sessionInfo’
COMPASS: multiple local function definitions for ‘.drop_degree_one’
  with different formal arguments
COMPASSContainerFromGatingSet: no visible global function definition
  for ‘pData’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous> :
  <anonymous>: no visible global function definition for ‘na.omit’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous> :
  <anonymous>: no visible global function definition for ‘parameters’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for ‘na.omit’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for ‘parameters’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for ‘getData’
COMPASSContainerFromGatingSet: no visible global function definition
  for ‘parameters’
COMPASSContainerFromGatingSet: no visible global function definition
  for ‘na.omit’
COMPASSContainerFromGatingSet: no visible global function definition
  for ‘getSingleCellExpression’
GetThresholdedIntensities: no visible global function definition for
  ‘parameters’
GetThresholdedIntensities : .check_match : <anonymous>: no visible
  global function definition for ‘na.omit’
GetThresholdedIntensities: no visible global function definition for
  ‘exprs’
GetThresholdedIntensities : <anonymous>: no visible global function
  definition for ‘getData’
MakeComparable: no visible global function definition for ‘combn’
TotalCellCounts: no visible global function definition for ‘setNames’
cluster_mat: no visible global function definition for ‘as.dist’
cluster_mat: no visible global function definition for ‘cor’
cluster_mat: no visible global function definition for ‘dist’
cluster_mat: no visible global function definition for ‘hclust’
draw_polar_legend: no visible binding for global variable ‘trtLabels’
generate_annotation_colours: no visible global function definition for
  ‘hsv’
generate_annotation_colours: no visible global function definition for
  ‘runif’
generate_row_annotation_colours: no visible global function definition
  for ‘hsv’
heatmap_motor : <anonymous>: no visible global function definition for
  ‘pdf’
heatmap_motor : <anonymous>: no visible global function definition for
  ‘png’
heatmap_motor : <anonymous>: no visible global function definition for
  ‘jpeg’
heatmap_motor : <anonymous>: no visible global function definition for
  ‘tiff’
heatmap_motor : <anonymous>: no visible global function definition for
  ‘bmp’
heatmap_motor: no visible global function definition for ‘dev.off’
kmeans_pheatmap: no visible binding for global variable ‘sd’
kmeans_pheatmap: no visible global function definition for ‘kmeans’
lo: no visible global function definition for ‘strwidth’
pheatmap: no visible global function definition for ‘kmeans’
plot.COMPASSResult: no visible global function definition for ‘is’
plot2: no visible global function definition for ‘colorRamp’
plot2: no visible global function definition for ‘rgb2hsv’
plot2: no visible global function definition for ‘hsv’
scale_colours: no visible global function definition for ‘rainbow’
scale_rows: no visible binding for global variable ‘sd’
scale_vec_colours: no visible global function definition for ‘rainbow’
shinyCOMPASS: no visible global function definition for ‘runApp’
shinyCOMPASSDeps: no visible global function definition for
  ‘installed.packages’
summary.COMPASSContainer: no visible global function definition for
  ‘hist’
Undefined global functions or variables:
  as.dist bmp colorRamp combn cor dev.off dist exprs getData
  getSingleCellExpression hclust head hist hsv installed.packages is
  jpeg kmeans median na.omit pData parameters pdf png rainbow rgb
  rgb2hsv runApp runif sd sessionInfo setNames strwidth tiff trtLabels
Consider adding
  importFrom("grDevices", "bmp", "colorRamp", "dev.off", "hsv", "jpeg",
             "pdf", "png", "rainbow", "rgb", "rgb2hsv", "tiff")
  importFrom("graphics", "hist", "strwidth")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "kmeans",
             "median", "na.omit", "runif", "sd", "setNames")
  importFrom("utils", "combn", "head", "installed.packages",
             "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/COMPASS.Rcheck/00check.log’
for details.


COMPASS.Rcheck/00install.out:

* installing *source* package ‘COMPASS’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c COMPASS_init.c -o COMPASS_init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c CellCounts.cpp -o CellCounts.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c CellCounts_character.cpp -o CellCounts_character.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c digamma.c -o digamma.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mat2vec.c -o mat2vec.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c melt_dataframe.c -o melt_dataframe.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c melt_matrix.c -o melt_matrix.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c samplePuPs.cpp -o samplePuPs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c transpose_list.c -o transpose_list.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updatealphas_Exp.cpp -o updatealphas_Exp.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updatealphau.cpp -o updatealphau.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updatebeta_RW.cpp -o updatebeta_RW.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c updategammak_noPu.cpp -o updategammak_noPu.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c utils.c -o utils.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o COMPASS.so COMPASS_init.o CellCounts.o CellCounts_character.o RcppExports.o digamma.o mat2vec.o melt_dataframe.o melt_matrix.o samplePuPs.o transpose_list.o updatealphas_Exp.o updatealphau.o updatealphau_noPu_Exp.o updatebeta_RW.o updategammak_noPu.o utils.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/COMPASS.Rcheck/COMPASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (COMPASS)

COMPASS.Rcheck/COMPASS-Ex.timings:

nameusersystemelapsed
COMPASS0.3600.0040.374
COMPASSContainer0.0320.0000.032
COMPASSContainerFromGatingSet000
CellCounts0.4800.0120.495
Combinations0.0000.0000.001
FunctionalityScore0.0040.0000.003
GetThresholdedIntensities2.8760.0402.962
PolyfunctionalityScore0.0040.0000.001
Posterior0.0040.0000.003
SimpleCOMPASS0.0000.0000.001
TotalCellCounts0.020.000.02
UniqueCombinations0.0040.0000.004
merge.COMPASSContainer0.0120.0000.013
pheatmap1.2680.0081.279
plot.COMPASSResult0.0960.0040.097
print.COMPASSContainer000
print.COMPASSResult000
scores0.0080.0000.007
shinyCOMPASS0.0040.0000.001
shinyCOMPASSDeps0.7800.0160.803
subset.COMPASSContainer0.0000.0000.002
summary.COMPASSContainer0.0040.0000.004
summary.COMPASSResult0.0000.0040.000
transpose_list0.0000.0000.001