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 ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings COMPASS_1.11.7.tar.gz
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* 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.
* 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)