Till Soerensen
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/immunoClust |
| git_branch: RELEASE_3_20 |
| git_last_commit: c4a056b |
| git_last_commit_date: 2024-10-29 09:59:09 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:04 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1021/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| immunoClust 1.38.0 (landing page) Till Soerensen
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.38.0 |
| 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_1.38.0.tar.gz |
| StartedAt: 2024-12-31 02:27:53 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 02:32:08 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 254.6 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/immunoClust.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.38.0'
* 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) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 ... NOTE
plot,immunoClust-missing: no visible global function definition for
'abline'
Undefined global functions or variables:
abline
Consider adding
importFrom("graphics", "abline")
to your NAMESPACE file.
* 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 98.18 0.26 98.46
cell.SubClustering 17.14 0.06 17.22
* 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: 2 NOTEs
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) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
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
hc_meta.cpp: In member function 'void mvn_dendro::init_D_diag(double)':
hc_meta.cpp:111:9: warning: unused variable 'status' [-Wunused-variable]
111 | int status = 0;
| ^~~~~~
hc_meta.cpp: In member function 'void mvn_dendro::update_D_diag(int, int, double)':
hc_meta.cpp:343:39: warning: unused variable 'status' [-Wunused-variable]
343 | int i, j, /*status_i, status_j,*/ status;
| ^~~~~~
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 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 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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
7.18 0.32 7.65
immunoClust.Rcheck/immunoClust-Ex.timings
| name | user | system | elapsed | |
| SON.clustering | 0.36 | 0.03 | 0.39 | |
| SON.combineClustering | 0.05 | 0.02 | 0.06 | |
| bhattacharyya | 0.01 | 0.00 | 0.01 | |
| cell.ClustData | 1.57 | 0.02 | 1.58 | |
| cell.EM | 1.15 | 0.01 | 1.17 | |
| cell.FitModel | 1.10 | 0.02 | 1.11 | |
| cell.ME | 0.82 | 0.00 | 0.83 | |
| cell.SubClustering | 17.14 | 0.06 | 17.22 | |
| cell.hclust | 0.00 | 0.00 | 0.08 | |
| cell.process | 98.18 | 0.26 | 98.46 | |
| cell.removed | 0.00 | 0.02 | 0.02 | |
| dat.exp | 0.20 | 0.00 | 0.22 | |
| dat.fcs | 0.03 | 0.00 | 0.03 | |
| dat.meta | 0.00 | 0.00 | 0.03 | |
| immunoClust.methods | 0.00 | 0.02 | 0.02 | |
| immunoClust.object | 0.02 | 0.00 | 0.01 | |
| immunoMeta.methods | 0 | 0 | 0 | |
| immunoMeta.object | 0.01 | 0.01 | 0.03 | |
| meta.ME | 0.03 | 0.00 | 0.04 | |
| meta.SubClustering | 0.05 | 0.00 | 0.04 | |
| meta.clustering | 0.14 | 0.02 | 0.15 | |
| meta.export | 0.14 | 0.00 | 0.14 | |
| meta.exprs | 0.01 | 0.00 | 0.02 | |
| meta.hclust | 0.00 | 0.01 | 0.02 | |
| meta.normalize | 0 | 0 | 0 | |
| meta.process | 0.16 | 0.00 | 0.16 | |
| meta.regnorm | 0 | 0 | 0 | |
| plot.immunoClust | 0.11 | 0.02 | 0.13 | |
| plot.immunoMeta | 2.10 | 0.08 | 2.18 | |
| splom.immunoClust | 1.26 | 0.03 | 1.29 | |
| trans.ApplyToData | 0.07 | 0.01 | 0.08 | |
| trans.FitToData | 0.26 | 0.02 | 0.28 | |