Package: COMPASS

Version: 1.16.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings COMPASS_1.16.2.tar.gz

StartedAt: 2018-04-12 02:06:05 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:08:37 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 151.9 seconds

RetCode: 0

Status:  OK

CheckDir: COMPASS.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings COMPASS_1.16.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/COMPASS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.2’
* 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
':::' call which should be '::': ‘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
COMPASSfitToCountsTable: no visible binding for global variable
  ‘population’
COMPASSfitToCountsTable: no visible binding for global variable ‘Count’
COMPASSfitToCountsTable: no visible binding for global variable ‘id’
Undefined global functions or variables:
  Count id population
* 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 shell scripts ... 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/COMPASS.Rcheck/00check.log’
for details.

* installing *source* package ‘COMPASS’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPASS_c.c -o COMPASS_c.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPASS_cpp.cpp -o COMPASS_cpp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPASS_init.c -o COMPASS_init.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 COMPASS.so COMPASS_c.o COMPASS_cpp.o COMPASS_init.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(COMPASS)
> if (file.exists("testthat")) {
+   test_dir("testthat")
+ }
✔ | OK F W S | Context

⠏ |  0       | COMPASS Interface
⠋ |  1       | COMPASS Interface
✔ |  1       | COMPASS Interface [1.3 s]

⠏ |  0       | test plotCOMPASSResultStack
⠋ |  1       | test plotCOMPASSResultStack
⠙ |  2       | test plotCOMPASSResultStack
⠹ |  3       | test plotCOMPASSResultStack
⠸ |  4       | test plotCOMPASSResultStack
⠼ |  5       | test plotCOMPASSResultStack
⠴ |  6       | test plotCOMPASSResultStack
✔ |  6       | test plotCOMPASSResultStack [70.6 s]

⠏ |  0       | CellCounts
⠋ |  1       | CellCounts
⠙ |  2       | CellCounts
⠹ |  3       | CellCounts
⠸ |  4       | CellCounts
⠼ |  5       | CellCounts
⠴ |  6       | CellCounts
⠦ |  7       | CellCounts
✔ |  7       | CellCounts

⠏ |  0       | FS, PFS
⠋ |  1       | FS, PFS
⠙ |  2       | FS, PFS
⠹ |  3       | FS, PFS
⠸ |  4       | FS, PFS
⠼ |  5       | FS, PFS
⠴ |  6       | FS, PFS
⠦ |  7       | FS, PFS
⠧ |  8       | FS, PFS
✔ |  8       | FS, PFS

⠏ |  0       | test COMPASSContainerFromGatingSet
⠋ |  1       | test COMPASSContainerFromGatingSet
⠙ |  2       | test COMPASSContainerFromGatingSet
⠹ |  3       | test COMPASSContainerFromGatingSet
⠸ |  4       | test COMPASSContainerFromGatingSet
⠼ |  5       | test COMPASSContainerFromGatingSet
⠴ |  6       | test COMPASSContainerFromGatingSet
⠦ |  7       | test COMPASSContainerFromGatingSet
✔ |  7       | test COMPASSContainerFromGatingSet [3.6 s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 76.0 s

OK:       29
Failed:   0
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 72.849   3.779  77.659 

name	user	system	elapsed
COMPASS	0.510	0.042	0.565
COMPASSContainer	0.058	0.001	0.054
COMPASSContainerFromGatingSet	0.001	0.000	0.001
CellCounts	0.836	0.073	0.685
Combinations	0.011	0.000	0.012
FunctionalityScore	0.004	0.001	0.006
GetThresholdedIntensities	3.774	0.142	3.787
PolyfunctionalityScore	0.001	0.000	0.001
Posterior	0.004	0.001	0.005
SimpleCOMPASS	4.405	0.262	4.730
TotalCellCounts	0.069	0.001	0.041
UniqueCombinations	0.059	0.002	0.032
getCounts	0.075	0.015	0.043
merge.COMPASSContainer	0.281	0.040	0.173
pheatmap	2.797	0.017	2.912
plot.COMPASSResult	0.288	0.002	0.295
plotCOMPASSResultStack	0.000	0.001	0.001
print.COMPASSContainer	0.000	0.000	0.001
print.COMPASSResult	0	0	0
scores	0.125	0.001	0.131
select_compass_pops	0.006	0.000	0.006
shinyCOMPASS	0.001	0.000	0.001
shinyCOMPASSDeps	1.075	0.082	1.209
subset.COMPASSContainer	0.002	0.000	0.002
summary.COMPASSContainer	0.004	0.000	0.004
summary.COMPASSResult	0.001	0.000	0.001
translate_marker_names	0.004	0.000	0.004
transpose_list	0.001	0.000	0.001