Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1008/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
immunoClust 1.37.11 (landing page) Till Soerensen
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the immunoClust package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immunoClust.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. |
Package: immunoClust |
Version: 1.37.11 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunoClust.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings immunoClust_1.37.11.tar.gz |
StartedAt: 2024-08-16 01:46:16 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 01:50:30 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 254.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: immunoClust.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunoClust.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings immunoClust_1.37.11.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/immunoClust.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'immunoClust/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'immunoClust' version '1.37.11' * 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 whether package 'immunoClust' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/immunoClust/libs/x64/immunoClust.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 cell.process 99.49 0.32 99.81 cell.SubClustering 17.33 0.11 17.46 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/immunoClust.Rcheck/00check.log' for details.
immunoClust.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL immunoClust ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'immunoClust' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_meta.cpp -o R_meta.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_model.cpp -o R_model.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dist_mvn.cpp -o dist_mvn.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_meta.cpp -o em_meta.o em_meta.cpp: In member function 'int em_meta::start(int*, bool)': em_meta.cpp:522:9: warning: variable 'status' set but not used [-Wunused-but-set-variable] 522 | int status = 0; | ^~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_meta_bc.cpp -o em_meta_bc.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_meta_kl.cpp -o em_meta_kl.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_mvn.cpp -o em_mvn.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_mvt.cpp -o em_mvt.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_mvt2.cpp -o em_mvt2.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hc_meta.cpp -o hc_meta.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hc_mvn.cpp -o hc_mvn.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c immunoClust.c -o immunoClust.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c meta_SON.cpp -o meta_SON.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c meta_norm.cpp -o meta_norm.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c meta_scale.cpp -o meta_scale.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model_scale.cpp -o model_scale.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c normalize.cpp -o normalize.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sub_mvn.cpp -o sub_mvn.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vs_htrans.cpp -o vs_htrans.o g++ -std=gnu++17 -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_meta_bc.o em_meta_kl.o em_mvn.o em_mvt.o em_mvt2.o hc_meta.o hc_mvn.o immunoClust.o meta_SON.o meta_norm.o meta_scale.o model_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-immunoClust/00new/immunoClust/libs/x64 ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (immunoClust)
immunoClust.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(immunoClust) Loading required package: flowCore > > test_check("immunoClust") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ] > > proc.time() user system elapsed 7.31 0.34 7.57
immunoClust.Rcheck/immunoClust-Ex.timings
name | user | system | elapsed | |
SON.clustering | 0.52 | 0.03 | 0.54 | |
SON.combineClustering | 0.07 | 0.00 | 0.06 | |
bhattacharyya | 0.01 | 0.00 | 0.02 | |
cell.ClustData | 1.47 | 0.05 | 1.51 | |
cell.EM | 1.22 | 0.04 | 1.28 | |
cell.FitModel | 1.14 | 0.02 | 1.16 | |
cell.ME | 0.67 | 0.00 | 0.67 | |
cell.SubClustering | 17.33 | 0.11 | 17.46 | |
cell.hclust | 0.00 | 0.01 | 0.01 | |
cell.process | 99.49 | 0.32 | 99.81 | |
cell.removed | 0.01 | 0.00 | 0.02 | |
dat.exp | 0.24 | 0.01 | 0.25 | |
dat.fcs | 0.03 | 0.00 | 0.03 | |
dat.meta | 0.00 | 0.02 | 0.02 | |
immunoClust.methods | 0.01 | 0.00 | 0.01 | |
immunoClust.object | 0.02 | 0.00 | 0.02 | |
immunoMeta.methods | 0 | 0 | 0 | |
immunoMeta.object | 0.01 | 0.01 | 0.03 | |
meta.ME | 0.05 | 0.00 | 0.05 | |
meta.SubClustering | 0.06 | 0.00 | 0.06 | |
meta.clustering | 0.41 | 0.00 | 0.40 | |
meta.export | 0.33 | 0.00 | 0.33 | |
meta.exprs | 0.00 | 0.02 | 0.02 | |
meta.hclust | 0.00 | 0.01 | 0.01 | |
meta.normalize | 0.00 | 0.02 | 0.02 | |
meta.process | 0.40 | 0.00 | 0.41 | |
meta.regnorm | 0.00 | 0.02 | 0.01 | |
plot.immunoClust | 0.11 | 0.00 | 0.11 | |
plot.immunoMeta | 2.16 | 0.07 | 2.24 | |
splom.immunoClust | 1.31 | 0.05 | 1.35 | |
trans.ApplyToData | 0.03 | 0.02 | 0.05 | |
trans.FitToData | 0.24 | 0.01 | 0.25 | |