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CHECK report for COMPASS on malbec1

This page was generated on 2021-05-06 12:27:13 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the COMPASS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 358/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.28.0  (landing page)
Greg Finak
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/COMPASS
Branch: RELEASE_3_12
Last Commit: f1557e7
Last Changed Date: 2020-10-27 10:54:46 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: COMPASS
Version: 1.28.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings COMPASS_1.28.0.tar.gz
StartedAt: 2021-05-06 00:20:25 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:22:48 -0400 (Thu, 06 May 2021)
EllapsedTime: 143.1 seconds
RetCode: 0
Status:   OK  
CheckDir: COMPASS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings COMPASS_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/COMPASS.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.28.0’
* package encoding: UTF-8
* 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 ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs    4.3Mb
    shiny   1.4Mb
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘rmarkdown’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.CellCounts: no visible binding for global variable
  ‘_COMPASS_CellCounts’
COMPASSfitToCountsTable: no visible binding for global variable
  ‘population’
COMPASSfitToCountsTable: no visible binding for global variable ‘Count’
COMPASSfitToCountsTable: no visible binding for global variable ‘id’
CellCounts_character: no visible binding for global variable
  ‘_COMPASS_CellCounts_character’
GetThresholdedIntensities : <anonymous>: no visible global function
  definition for ‘gh_pop_is_bool_gate’
Undefined global functions or variables:
  Count _COMPASS_CellCounts _COMPASS_CellCounts_character
  gh_pop_is_bool_gate 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
GetThresholdedIntensities 5.852    0.1   6.036
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/COMPASS.Rcheck/00check.log’
for details.



Installation output

COMPASS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL COMPASS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘COMPASS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c COMPASS_init.c -o COMPASS_init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c CellCounts.cpp -o CellCounts.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c CellCounts_character.cpp -o CellCounts_character.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c digamma.c -o digamma.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mat2vec.c -o mat2vec.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c melt_dataframe.c -o melt_dataframe.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c melt_matrix.c -o melt_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c samplePuPs.cpp -o samplePuPs.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c transpose_list.c -o transpose_list.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updatealphas_Exp.cpp -o updatealphas_Exp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updatealphau.cpp -o updatealphau.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updatebeta_RW.cpp -o updatebeta_RW.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updategammak_noPu.cpp -o updategammak_noPu.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-COMPASS/00new/COMPASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COMPASS)

Tests output

COMPASS.Rcheck/tests/test-all.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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                                                         
⠏ |   0       | COMPASS Interface                                               
⠋ |   1       | COMPASS Interface                                               
✔ |   1       | COMPASS Interface [0.7 s]

⠏ |   0       | COMPASSPlot                                                     
⠏ |   0       | test plotCOMPASSResultStack                                     
⠋ |   1       | test plotCOMPASSResultStack                                     
⠹ |   3       | test plotCOMPASSResultStack                                     
⠴ |   6       | test plotCOMPASSResultStack                                     
✔ |   6       | test plotCOMPASSResultStack [61.1 s]

⠏ |   0       | CellCounts                                                      
⠏ |   0       | CellCounts                                                      
✔ |   7       | CellCounts

⠏ |   0       | FunctionalityScore                                              
⠏ |   0       | FS, PFS                                                         
✔ |   8       | FS, PFS

⠏ |   0       | GatingSet2COMPASS                                               
⠏ |   0       | test COMPASSContainerFromGatingSet                              
⠋ |   0   1   | test COMPASSContainerFromGatingSet                              
⠙ |   1   1   | test COMPASSContainerFromGatingSet                              
⠴ |   5   1   | test COMPASSContainerFromGatingSet                              
✔ |   7   1   | test COMPASSContainerFromGatingSet [4.2 s]
────────────────────────────────────────────────────────────────────────────────
Warning (test-GatingSet2COMPASS.R:8:1): (code run outside of `test_that()`)
'GatingSetList' is deprecated.
Use 'merge_list_to_gs' instead.
See help("Deprecated")
Backtrace:
 1. flowWorkspace::merge_list_to_gs(GatingSetList(list(gs1, gs2))) test-GatingSet2COMPASS.R:8:0
 3. flowWorkspace::GatingSetList(list(gs1, gs2))
 4. base::.Deprecated("merge_list_to_gs")
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 66.0 s

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 68.372   0.392  68.828 

Example timings

COMPASS.Rcheck/COMPASS-Ex.timings

nameusersystemelapsed
COMPASS0.3000.0120.305
COMPASSContainer0.0680.0000.069
COMPASSContainerFromGatingSet000
CellCounts0.4960.0240.522
Combinations0.0000.0000.001
FunctionalityScore0.0040.0000.005
GetThresholdedIntensities5.8520.1006.036
PolyfunctionalityScore0.0000.0000.001
Posterior0.0000.0040.004
Response0.0200.0000.023
SimpleCOMPASS2.9280.0082.939
TotalCellCounts0.0200.0000.017
UniqueCombinations0.0040.0000.003
checkCOMPASSConvergence0.3640.0040.378
getCounts0.0440.0000.044
merge.COMPASSContainer0.0120.0000.013
pheatmap1.0400.0081.045
plot.COMPASSResult0.0480.0000.048
plotCOMPASSResultStack000
print.COMPASSContainer0.0000.0000.001
print.COMPASSResult0.0000.0000.001
scores0.0040.0000.007
select_compass_pops0.0040.0000.004
shinyCOMPASS000
shinyCOMPASSDeps2.3080.0682.413
subset.COMPASSContainer0.0040.0000.002
summary.COMPASSContainer0.0040.0000.005
summary.COMPASSResult000
translate_marker_names0.0040.0000.003
transpose_list000