Greg Finak
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/COMPASS |
| git_branch: RELEASE_3_21 |
| git_last_commit: a60809c |
| git_last_commit_date: 2025-04-15 10:28:48 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 422/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COMPASS 1.46.0 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the COMPASS package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: COMPASS |
| Version: 1.46.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COMPASS_1.46.0.tar.gz |
| StartedAt: 2025-10-14 07:43:14 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 07:45:29 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 135.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COMPASS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:COMPASS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COMPASS_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/COMPASS.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COMPASS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COMPASS’ version ‘1.46.0’
* 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
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
installed size is 8.4Mb
sub-directories of 1Mb or more:
libs 6.2Mb
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 code 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 whether startup messages can be suppressed ... 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
File ‘COMPASS/libs/COMPASS.so’:
Found non-API call to R: ‘STRING_PTR’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GetThresholdedIntensities 5.301 0.263 5.581
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/COMPASS.Rcheck/00check.log’
for details.
COMPASS.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL COMPASS
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘COMPASS’ ...
** this is package ‘COMPASS’ version ‘1.46.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c COMPASS_init.c -o COMPASS_init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c CellCounts.cpp -o CellCounts.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c CellCounts_character.cpp -o CellCounts_character.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c digamma.c -o digamma.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c mat2vec.c -o mat2vec.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c melt_dataframe.c -o melt_dataframe.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c melt_matrix.c -o melt_matrix.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c samplePuPs.cpp -o samplePuPs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c transpose_list.c -o transpose_list.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c updatealphas_Exp.cpp -o updatealphas_Exp.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c updatealphas_Exp_MH.cpp -o updatealphas_Exp_MH.o
updatealphas_Exp_MH.cpp: In function ‘SEXPREC* updatealphas_Exp_MH(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
updatealphas_Exp_MH.cpp:26:10: warning: variable ‘psik’ set but not used [-Wunused-but-set-variable]
26 | double psik = 0.;
| ^~~~
updatealphas_Exp_MH.cpp:35:7: warning: variable ‘flagkk’ set but not used [-Wunused-but-set-variable]
35 | int flagkk = 0;
| ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c updatealphau.cpp -o updatealphau.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c updatealphau_noPu_Exp_MH.cpp -o updatealphau_noPu_Exp_MH.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c updatebeta_RW.cpp -o updatebeta_RW.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c updategammak_noPu.cpp -o updategammak_noPu.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/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 updatealphas_Exp_MH.o updatealphau.o updatealphau_noPu_Exp.o updatealphau_noPu_Exp_MH.o updatebeta_RW.o updategammak_noPu.o utils.o -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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 [1.2s]
⠏ | 0 | COMPASSPlot
⠏ | 0 | test plotCOMPASSResultStack
⠋ | 1 | test plotCOMPASSResultStack
⠹ | 3 | test plotCOMPASSResultStack
✔ | 6 | test plotCOMPASSResultStack [56.3s]
⠏ | 0 | CellCounts
⠏ | 0 | CellCounts
✔ | 7 | CellCounts
⠏ | 0 | FunctionalityScore
⠏ | 0 | FS, PFS
✔ | 8 | FS, PFS
⠏ | 0 | GatingSet2COMPASS
⠏ | 0 | test COMPASSContainerFromGatingSet
⠋ | 1 0 | test COMPASSContainerFromGatingSet
⠼ | 1 4 | test COMPASSContainerFromGatingSet
⠴ | 2 4 | test COMPASSContainerFromGatingSet
✔ | 2 7 | test COMPASSContainerFromGatingSet
────────────────────────────────────────────────────────────────────────────────
Warning ('test-GatingSet2COMPASS.R:15:3'): COMPASSContainerFromGatingSet
There appear to be negative intensities in the 'data' supplied.
Backtrace:
▆
1. └─COMPASS::COMPASSContainerFromGatingSet(...) at test-GatingSet2COMPASS.R:15:3
2. └─COMPASS::COMPASSContainer(...)
Warning ('test-GatingSet2COMPASS.R:30:3'): COMPASSContainerFromGatingSet
There appear to be negative intensities in the 'data' supplied.
Backtrace:
▆
1. └─COMPASS::COMPASSContainerFromGatingSet(...) at test-GatingSet2COMPASS.R:30:3
2. └─COMPASS::COMPASSContainer(...)
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 58.4 s
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ]
>
> proc.time()
user system elapsed
63.675 0.816 64.430
COMPASS.Rcheck/COMPASS-Ex.timings
| name | user | system | elapsed | |
| COMPASS | 0.196 | 0.008 | 0.365 | |
| COMPASSContainer | 0.055 | 0.020 | 0.075 | |
| COMPASSContainerFromGatingSet | 0 | 0 | 0 | |
| CellCounts | 0.426 | 0.028 | 0.449 | |
| Combinations | 0 | 0 | 0 | |
| FunctionalityScore | 0.005 | 0.000 | 0.005 | |
| GetThresholdedIntensities | 5.301 | 0.263 | 5.581 | |
| PolyfunctionalityScore | 0.000 | 0.000 | 0.001 | |
| Posterior | 0.002 | 0.000 | 0.002 | |
| Response | 0.002 | 0.008 | 0.011 | |
| SimpleCOMPASS | 2.304 | 0.096 | 2.405 | |
| TotalCellCounts | 0.027 | 0.000 | 0.026 | |
| UniqueCombinations | 0.006 | 0.000 | 0.006 | |
| getCounts | 0.059 | 0.004 | 0.062 | |
| merge.COMPASSContainer | 0.016 | 0.000 | 0.016 | |
| pheatmap | 1.270 | 0.060 | 1.333 | |
| plot.COMPASSResult | 0.068 | 0.000 | 0.068 | |
| plotCOMPASSResultStack | 0 | 0 | 0 | |
| print.COMPASSContainer | 0 | 0 | 0 | |
| print.COMPASSResult | 0 | 0 | 0 | |
| scores | 0.01 | 0.00 | 0.01 | |
| select_compass_pops | 0.006 | 0.000 | 0.006 | |
| shinyCOMPASS | 0 | 0 | 0 | |
| shinyCOMPASSDeps | 0.839 | 0.040 | 0.881 | |
| subset.COMPASSContainer | 0.002 | 0.000 | 0.002 | |
| summary.COMPASSContainer | 0.005 | 0.000 | 0.005 | |
| summary.COMPASSResult | 0 | 0 | 0 | |
| translate_marker_names | 0.002 | 0.000 | 0.002 | |
| transpose_list | 0 | 0 | 0 | |