Greg Finak
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/COMPASS |
| Branch: RELEASE_3_11 |
| Last Commit: 095d94d |
| Last Changed Date: 2020-04-27 14:38:26 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:58:17 -0400 (Sat, 17 Oct 2020).
| 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 355/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| COMPASS 1.26.0 Greg Finak
| malbec2 | Linux (Ubuntu 18.04.4 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: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2020-10-16 23:57:45 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-17 00:00:39 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 173.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COMPASS.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/COMPASS.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.26.0’
* 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:
.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’
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 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 5.309 0.252 5.634
* 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-3.11-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/4.0/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/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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++11 -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-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/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
> if (file.exists("testthat")) {
+ test_dir("testthat")
+ }
✔ | OK F W S | Context
⠏ | 0 | COMPASS Interface
⠋ | 1 | COMPASS Interface
✔ | 1 | COMPASS Interface [0.9 s]
⠏ | 0 | test plotCOMPASSResultStack
⠋ | 1 | test plotCOMPASSResultStack
✖ | 4 2 | test plotCOMPASSResultStack [71.2 s]
────────────────────────────────────────────────────────────────────────────────
test-COMPASSPlot.R:96: failure: only COMPASSResults with the same markers can be stacked
`plotCOMPASSResultStack(...)` threw an error.
Message: object not specified
Class: simpleError/error/condition
Backtrace:
1. testthat::expect_error(...) test-COMPASSPlot.R:96:2
6. COMPASS::plotCOMPASSResultStack(...)
7. COMPASS:::mergeMatricesForPlotCOMPASSResultStack(...)
8. base::as.matrix.noquote(catsMerged[, "Counts"])
10. base::NextMethod("as.matrix", x)
test-COMPASSPlot.R:199: error: mergeMatricesForPlotCOMPASSResultStack merges mean_gamma matrices correctly
object not specified
Backtrace:
1. COMPASS:::mergeMatricesForPlotCOMPASSResultStack(...) test-COMPASSPlot.R:199:2
2. base::as.matrix.noquote(catsMerged[, "Counts"])
4. base::NextMethod("as.matrix", x)
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | CellCounts
✔ | 7 | CellCounts
⠏ | 0 | FS, PFS
✔ | 8 | FS, PFS
⠏ | 0 | test COMPASSContainerFromGatingSet
⠋ | 0 1 | test COMPASSContainerFromGatingSet
✖ | 0 1 3 | test COMPASSContainerFromGatingSet [2.8 s]
────────────────────────────────────────────────────────────────────────────────
test-GatingSet2COMPASS.R:5: warning: (unknown)
'clone' is deprecated.
Use 'gs_clone' instead.
See help("Deprecated")
test-GatingSet2COMPASS.R:6: warning: (unknown)
'clone' is deprecated.
Use 'gs_clone' instead.
See help("Deprecated")
test-GatingSet2COMPASS.R:8: warning: (unknown)
'GatingSetList' is deprecated.
Use 'merge_list_to_gs' instead.
See help("Deprecated")
test-GatingSet2COMPASS.R:8: error: (unknown)
'rbind2' is defunct.
Use 'merge_list_to_gs' instead.
See help("Defunct")
Backtrace:
1. methods::rbind2(GatingSetList(list(gs1, gs2))) test-GatingSet2COMPASS.R:8:0
2. flowWorkspace::rbind2(GatingSetList(list(gs1, gs2)))
3. base::.Defunct("merge_list_to_gs")
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 75.1 s
OK: 20
Failed: 3
Warnings: 3
Skipped: 0
>
> proc.time()
user system elapsed
77.388 1.123 78.668
COMPASS.Rcheck/COMPASS-Ex.timings
| name | user | system | elapsed | |
| COMPASS | 0.306 | 0.031 | 0.339 | |
| COMPASSContainer | 0.071 | 0.003 | 0.073 | |
| COMPASSContainerFromGatingSet | 0.001 | 0.000 | 0.000 | |
| CellCounts | 0.520 | 0.048 | 0.567 | |
| Combinations | 0.001 | 0.001 | 0.002 | |
| FunctionalityScore | 0.006 | 0.001 | 0.007 | |
| GetThresholdedIntensities | 5.309 | 0.252 | 5.634 | |
| PolyfunctionalityScore | 0.001 | 0.000 | 0.002 | |
| Posterior | 0.004 | 0.004 | 0.008 | |
| Response | 0.010 | 0.001 | 0.011 | |
| SimpleCOMPASS | 3.607 | 0.055 | 3.674 | |
| TotalCellCounts | 0.028 | 0.002 | 0.029 | |
| UniqueCombinations | 0.005 | 0.002 | 0.007 | |
| getCounts | 0.024 | 0.003 | 0.027 | |
| merge.COMPASSContainer | 0.014 | 0.002 | 0.015 | |
| pheatmap | 1.254 | 0.020 | 1.278 | |
| plot.COMPASSResult | 0.054 | 0.002 | 0.056 | |
| plotCOMPASSResultStack | 0.001 | 0.000 | 0.000 | |
| print.COMPASSContainer | 0.001 | 0.000 | 0.001 | |
| print.COMPASSResult | 0 | 0 | 0 | |
| scores | 0.007 | 0.000 | 0.007 | |
| select_compass_pops | 0.006 | 0.001 | 0.007 | |
| shinyCOMPASS | 0.001 | 0.001 | 0.001 | |
| shinyCOMPASSDeps | 2.647 | 0.494 | 3.181 | |
| subset.COMPASSContainer | 0.002 | 0.000 | 0.003 | |
| summary.COMPASSContainer | 0.007 | 0.002 | 0.008 | |
| summary.COMPASSResult | 0 | 0 | 0 | |
| translate_marker_names | 0.004 | 0.001 | 0.004 | |
| transpose_list | 0 | 0 | 0 | |