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This page was generated on 2024-03-27 11:36:52 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 1012/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunoClust 1.35.1  (landing page)
Till Soerensen
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/immunoClust
git_branch: devel
git_last_commit: c1401dd
git_last_commit_date: 2024-03-22 09:29:12 -0400 (Fri, 22 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for immunoClust on nebbiolo1


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.

raw results


Summary

Package: immunoClust
Version: 1.35.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings immunoClust_1.35.1.tar.gz
StartedAt: 2024-03-26 23:26:06 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 23:31:59 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 352.3 seconds
RetCode: 0
Status:   OK  
CheckDir: immunoClust.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings immunoClust_1.35.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/immunoClust.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘immunoClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunoClust’ version ‘1.35.1’
* 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 ‘immunoClust’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 is not available
File ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/immunoClust/libs/immunoClust.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
cell.process       78.379  0.008  78.388
cell.SubClustering 13.101  0.020  13.121
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/immunoClust.Rcheck/00check.log’
for details.


Installation output

immunoClust.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL immunoClust
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘immunoClust’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c R_meta.cpp -o R_meta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c R_model.cpp -o R_model.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c dist_mvn.cpp -o dist_mvn.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c em_meta.cpp -o em_meta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c em_meta_bc.cpp -o em_meta_bc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c em_meta_kl.cpp -o em_meta_kl.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c em_mvn.cpp -o em_mvn.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c em_mvt.cpp -o em_mvt.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c em_mvt2.cpp -o em_mvt2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c hc_meta.cpp -o hc_meta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c hc_mvn.cpp -o hc_mvn.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c immunoClust.c -o immunoClust.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c meta_SON.cpp -o meta_SON.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c meta_norm.cpp -o meta_norm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c meta_scale.cpp -o meta_scale.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c model_scale.cpp -o model_scale.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c normalize.cpp -o normalize.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c sub_mvn.cpp -o sub_mvn.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c util.cpp -o util.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c vs_htrans.cpp -o vs_htrans.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o immunoClust.so 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 -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-immunoClust/00new/immunoClust/libs
** 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
** 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 (immunoClust)

Tests output

immunoClust.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(immunoClust)
Loading required package: flowCore
> 
> test_check("immunoClust")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  6.893   0.229   7.111 

Example timings

immunoClust.Rcheck/immunoClust-Ex.timings

nameusersystemelapsed
SON.clustering1.8100.0481.858
SON.combineClustering0.0660.0000.066
bhattacharyya0.0050.0000.005
cell.ClustData1.1040.0191.122
cell.EM0.6360.0000.637
cell.FitModel0.5900.0080.598
cell.ME0.4490.0160.465
cell.SubClustering13.101 0.02013.121
cell.hclust0.0070.0000.006
cell.process78.379 0.00878.388
cell.removed0.010.000.01
dat.exp0.6350.0030.639
dat.fcs0.0130.0070.020
dat.meta0.0050.0000.005
immunoClust.methods0.0030.0000.003
immunoClust.object0.0050.0000.005
immunoMeta.methods0.0040.0000.004
immunoMeta.object0.0080.0040.012
meta.ME0.0080.0040.012
meta.SubClustering0.0940.0000.094
meta.clustering0.5830.0000.583
meta.export0.780.000.78
meta.exprs0.0080.0000.009
meta.hclust0.0040.0000.004
meta.normalize0.0030.0000.002
meta.process0.7680.0030.771
meta.regnorm0.0060.0000.005
plot.immunoClust0.0830.0000.083
plot.immunoMeta1.6970.0241.722
splom.immunoClust1.1340.0081.142
trans.ApplyToData0.0480.0000.048
trans.FitToData0.1370.0040.141