Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 415/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COMPASS 1.44.0 (landing page) Greg Finak
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.44.0 |
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_1.44.0.tar.gz |
StartedAt: 2024-11-20 06:29:40 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 06:31:57 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 137.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COMPASS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/COMPASS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (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 ‘1.44.0’ * 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: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ * used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking installed package size ... NOTE 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 * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GetThresholdedIntensities 5.046 0.2 5.268 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/COMPASS.Rcheck/00check.log’ for details.
COMPASS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL COMPASS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘COMPASS’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c COMPASS_init.c -o COMPASS_init.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c CellCounts.cpp -o CellCounts.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c CellCounts_character.cpp -o CellCounts_character.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c digamma.c -o digamma.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c mat2vec.c -o mat2vec.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c melt_dataframe.c -o melt_dataframe.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c melt_matrix.c -o melt_matrix.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c samplePuPs.cpp -o samplePuPs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c transpose_list.c -o transpose_list.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c updatealphas_Exp.cpp -o updatealphas_Exp.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -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; | ^~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c updatealphau.cpp -o updatealphau.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c updatealphau_noPu_Exp.cpp -o updatealphau_noPu_Exp.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c updatealphau_noPu_Exp_MH.cpp -o updatealphau_noPu_Exp_MH.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c updatebeta_RW.cpp -o updatebeta_RW.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c updategammak_noPu.cpp -o updategammak_noPu.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/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 -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 [58.0s] ⠏ | 0 | CellCounts ⠏ | 0 | CellCounts ✔ | 7 | CellCounts ⠏ | 0 | FunctionalityScore ⠏ | 0 | FS, PFS ✔ | 8 | FS, PFS ⠏ | 0 | GatingSet2COMPASS ⠏ | 0 | test COMPASSContainerFromGatingSet ⠋ | 1 | test COMPASSContainerFromGatingSet ⠼ | 1 4 | test COMPASSContainerFromGatingSet ✔ | 1 7 | test COMPASSContainerFromGatingSet ──────────────────────────────────────────────────────────────────────────────── 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: 60.1 s [ FAIL 0 | WARN 1 | SKIP 0 | PASS 29 ] > > proc.time() user system elapsed 64.843 1.060 65.878
COMPASS.Rcheck/COMPASS-Ex.timings
name | user | system | elapsed | |
COMPASS | 0.208 | 0.005 | 0.290 | |
COMPASSContainer | 0.057 | 0.000 | 0.057 | |
COMPASSContainerFromGatingSet | 0 | 0 | 0 | |
CellCounts | 0.421 | 0.012 | 0.428 | |
Combinations | 0.001 | 0.000 | 0.001 | |
FunctionalityScore | 0.004 | 0.000 | 0.004 | |
GetThresholdedIntensities | 5.046 | 0.200 | 5.268 | |
PolyfunctionalityScore | 0.000 | 0.000 | 0.001 | |
Posterior | 0.002 | 0.000 | 0.002 | |
Response | 0.009 | 0.000 | 0.009 | |
SimpleCOMPASS | 2.377 | 0.031 | 2.415 | |
TotalCellCounts | 0.023 | 0.001 | 0.022 | |
UniqueCombinations | 0.015 | 0.000 | 0.015 | |
getCounts | 0.034 | 0.004 | 0.038 | |
merge.COMPASSContainer | 0.012 | 0.000 | 0.012 | |
pheatmap | 1.240 | 0.015 | 1.261 | |
plot.COMPASSResult | 0.069 | 0.000 | 0.069 | |
plotCOMPASSResultStack | 0 | 0 | 0 | |
print.COMPASSContainer | 0.000 | 0.000 | 0.001 | |
print.COMPASSResult | 0 | 0 | 0 | |
scores | 0.009 | 0.000 | 0.008 | |
select_compass_pops | 0.004 | 0.000 | 0.005 | |
shinyCOMPASS | 0 | 0 | 0 | |
shinyCOMPASSDeps | 0.818 | 0.032 | 0.853 | |
subset.COMPASSContainer | 0.002 | 0.000 | 0.002 | |
summary.COMPASSContainer | 0.000 | 0.004 | 0.004 | |
summary.COMPASSResult | 0 | 0 | 0 | |
translate_marker_names | 0.002 | 0.000 | 0.002 | |
transpose_list | 0 | 0 | 0 | |