Greg Finak
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/COMPASS |
| git_branch: RELEASE_3_13 |
| git_last_commit: 00c36c3 |
| git_last_commit_date: 2021-05-19 12:02:54 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the COMPASS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COMPASS.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 368/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COMPASS 1.30.0 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: COMPASS |
| Version: 1.30.0 |
| 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_1.30.0.tar.gz |
| StartedAt: 2021-10-14 17:41:34 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:44:10 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 155.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COMPASS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/COMPASS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.30.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
.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’ ‘foreach’ ‘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 LazyData ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GetThresholdedIntensities 6.057 0.324 6.433
* 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-3.13-bioc/meat/COMPASS.Rcheck/00check.log’
for details.
COMPASS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL COMPASS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘COMPASS’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c COMPASS_init.c -o COMPASS_init.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c CellCounts.cpp -o CellCounts.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c CellCounts_character.cpp -o CellCounts_character.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c digamma.c -o digamma.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mat2vec.c -o mat2vec.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c melt_dataframe.c -o melt_dataframe.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c melt_matrix.c -o melt_matrix.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c samplePuPs.cpp -o samplePuPs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c transpose_list.c -o transpose_list.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c updatealphas_Exp.cpp -o updatealphas_Exp.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c updatealphas_Exp_MH.cpp -o updatealphas_Exp_MH.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c updatealphau.cpp -o updatealphau.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c updatealphau_noPu_Exp_MH.cpp -o updatealphau_noPu_Exp_MH.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c updatebeta_RW.cpp -o updatebeta_RW.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c updategammak_noPu.cpp -o updategammak_noPu.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 updatealphas_Exp_MH.o updatealphau.o updatealphau_noPu_Exp.o updatealphau_noPu_Exp_MH.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-darwin18/8.2.0 -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/4.1/Resources/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)
COMPASS.Rcheck/tests/test-all.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
> library(flowWorkspace)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:
vignette("flowWorkspace-Introduction", "flowWorkspace")
> if (file.exists("testthat")) {
+ test_dir("testthat")
+ }
✔ | F W S OK | Context
⠏ | 0 | COMPASS
⠏ | 0 | COMPASS Interface
⠋ | 1 | COMPASS Interface
✔ | 1 | COMPASS Interface [1.1s]
⠏ | 0 | COMPASSPlot
⠏ | 0 | test plotCOMPASSResultStack
⠋ | 1 | test plotCOMPASSResultStack
⠹ | 3 | test plotCOMPASSResultStack
✔ | 6 | test plotCOMPASSResultStack [62.8s]
⠏ | 0 | CellCounts
⠏ | 0 | CellCounts
✔ | 7 | CellCounts
⠏ | 0 | FunctionalityScore
⠏ | 0 | FS, PFS
✔ | 8 | FS, PFS
⠏ | 0 | GatingSet2COMPASS
⠏ | 0 | test COMPASSContainerFromGatingSet
⠋ | 1 | test COMPASSContainerFromGatingSet
⠼ | 5 | test COMPASSContainerFromGatingSet
✔ | 7 | test COMPASSContainerFromGatingSet [0.7s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 64.7 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
70.156 1.260 71.456
COMPASS.Rcheck/COMPASS-Ex.timings
| name | user | system | elapsed | |
| COMPASS | 0.309 | 0.016 | 0.326 | |
| COMPASSContainer | 0.049 | 0.002 | 0.051 | |
| COMPASSContainerFromGatingSet | 0.001 | 0.000 | 0.000 | |
| CellCounts | 0.463 | 0.048 | 0.511 | |
| Combinations | 0.001 | 0.001 | 0.002 | |
| FunctionalityScore | 0.005 | 0.001 | 0.007 | |
| GetThresholdedIntensities | 6.057 | 0.324 | 6.433 | |
| PolyfunctionalityScore | 0.001 | 0.000 | 0.001 | |
| Posterior | 0.002 | 0.002 | 0.004 | |
| Response | 0.01 | 0.00 | 0.01 | |
| SimpleCOMPASS | 3.585 | 0.033 | 3.618 | |
| TotalCellCounts | 0.023 | 0.001 | 0.023 | |
| UniqueCombinations | 0.005 | 0.001 | 0.006 | |
| getCounts | 0.033 | 0.005 | 0.038 | |
| merge.COMPASSContainer | 0.014 | 0.002 | 0.015 | |
| pheatmap | 1.096 | 0.018 | 1.122 | |
| plot.COMPASSResult | 0.080 | 0.002 | 0.083 | |
| plotCOMPASSResultStack | 0.000 | 0.000 | 0.001 | |
| print.COMPASSContainer | 0.000 | 0.000 | 0.001 | |
| print.COMPASSResult | 0.000 | 0.000 | 0.001 | |
| scores | 0.012 | 0.000 | 0.012 | |
| select_compass_pops | 0.007 | 0.001 | 0.008 | |
| shinyCOMPASS | 0.000 | 0.000 | 0.001 | |
| shinyCOMPASSDeps | 2.735 | 0.474 | 3.209 | |
| subset.COMPASSContainer | 0.001 | 0.000 | 0.001 | |
| summary.COMPASSContainer | 0.003 | 0.001 | 0.004 | |
| summary.COMPASSResult | 0 | 0 | 0 | |
| translate_marker_names | 0.002 | 0.001 | 0.002 | |
| transpose_list | 0.001 | 0.000 | 0.000 | |