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CHECK report for COMPASS on merida1

This page was generated on 2019-04-16 11:57:27 -0400 (Tue, 16 Apr 2019).

Package 310/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.20.1
Greg Finak
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/COMPASS
Branch: RELEASE_3_8
Last Commit: 8c13ec8
Last Changed Date: 2019-01-04 13:25:59 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: COMPASS
Version: 1.20.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings COMPASS_1.20.1.tar.gz
StartedAt: 2019-04-15 23:09:40 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:11:16 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 96.3 seconds
RetCode: 0
Status:  OK 
CheckDir: COMPASS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings COMPASS_1.20.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/COMPASS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.20.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘rmarkdown’
  All declared Imports should be used.
':::' 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
.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’
Undefined global functions or variables:
  Count _COMPASS_CellCounts _COMPASS_CellCounts_character 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GetThresholdedIntensities 4.151  0.925   3.891
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/COMPASS.Rcheck/00check.log’
for details.



Installation output

COMPASS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL COMPASS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘COMPASS’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c COMPASS_init.c -o COMPASS_init.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c CellCounts.cpp -o CellCounts.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c CellCounts_character.cpp -o CellCounts_character.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c digamma.c -o digamma.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c mat2vec.c -o mat2vec.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c melt_dataframe.c -o melt_dataframe.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c melt_matrix.c -o melt_matrix.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c samplePuPs.cpp -o samplePuPs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c transpose_list.c -o transpose_list.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updatealphas_Exp.cpp -o updatealphas_Exp.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updatealphau.cpp -o updatealphau.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updatebeta_RW.cpp -o updatebeta_RW.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c updategammak_noPu.cpp -o updategammak_noPu.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.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_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/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (COMPASS)

Tests output

COMPASS.Rcheck/tests/test-all.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 [0.8 s]

⠏ |  0       | test plotCOMPASSResultStack
⠋ |  0 1     | test plotCOMPASSResultStack
✖ |  0 1     | test plotCOMPASSResultStack [25.2 s]
────────────────────────────────────────────────────────────────────────────────
test-COMPASSPlot.R:58: error: (unknown)
Expecting a single value: [extent=2].
1: generateCompassResultExample(2, k = 8) at testthat/test-COMPASSPlot.R:58
2: COMPASS(CC, treatment = trt == "Treatment", control = trt == "Control", iterations = 100) at testthat/test-COMPASSPlot.R:46
3: .COMPASS.discrete(n_s = n_s, n_u = n_u, categories = categories, iterations = iterations, 
       replications = replications, verbose = verbose, ...)
────────────────────────────────────────────────────────────────────────────────

⠏ |  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: 29.8 s

OK:       23
Failed:   1
Warnings: 0
Skipped:  0
> 
> proc.time()
   user  system elapsed 
 34.833   5.570  31.473 

Example timings

COMPASS.Rcheck/COMPASS-Ex.timings

nameusersystemelapsed
COMPASS0.8671.2470.338
COMPASSContainer0.2490.3180.083
COMPASSContainerFromGatingSet0.0010.0010.000
CellCounts2.4370.4950.562
Combinations0.0010.0000.002
FunctionalityScore0.0030.0010.003
GetThresholdedIntensities4.1510.9253.891
PolyfunctionalityScore0.0010.0000.001
Posterior0.0040.0020.007
SimpleCOMPASS3.2870.0843.413
TotalCellCounts0.1340.1460.044
UniqueCombinations0.0260.0280.008
getCounts0.1060.1340.035
merge.COMPASSContainer0.0430.0560.014
pheatmap1.9620.5671.700
plot.COMPASSResult0.1030.0030.105
plotCOMPASSResultStack000
print.COMPASSContainer0.0000.0000.001
print.COMPASSResult000
scores0.0600.0630.023
select_compass_pops0.0220.0260.007
shinyCOMPASS0.0030.0040.001
shinyCOMPASSDeps2.4470.8492.271
subset.COMPASSContainer0.0010.0000.001
summary.COMPASSContainer0.0020.0010.004
summary.COMPASSResult0.0010.0000.000
translate_marker_names0.0030.0010.003
transpose_list0.0010.0000.000