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This page was generated on 2022-04-13 12:05:29 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for immunoClust on nebbiolo2


To the developers/maintainers of the immunoClust package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 926/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunoClust 1.26.0  (landing page)
Till Soerensen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/immunoClust
git_branch: RELEASE_3_14
git_last_commit: fe68208
git_last_commit_date: 2021-10-26 12:19:10 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: immunoClust
Version: 1.26.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings immunoClust_1.26.0.tar.gz
StartedAt: 2022-04-12 07:52:11 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:56:24 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 253.2 seconds
RetCode: 0
Status:   OK  
CheckDir: immunoClust.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings immunoClust_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/immunoClust.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘immunoClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘immunoClust’ version ‘1.26.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘immunoClust’ can be installed ... OK
* 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 R 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
dat.fcs            88.600  0.009  88.610
cell.process       81.659  0.043  81.705
cell.SubClustering 13.013  0.191  13.205
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/immunoClust.Rcheck/00check.log’
for details.



Installation output

immunoClust.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL immunoClust
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_meta.cpp -o R_meta.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_model.cpp -o R_model.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dist_mvn.cpp -o dist_mvn.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function ‘double em_meta::et_step()’:
em_meta.cpp:412:16: warning: variable ‘sndLike’ set but not used [-Wunused-but-set-variable]
  412 |         double sndLike = 0.0;
      |                ^~~~~~~
em_meta.cpp: In member function ‘double em_meta::fixedN_et_step()’:
em_meta.cpp:697:16: warning: variable ‘maxLike’ set but not used [-Wunused-but-set-variable]
  697 |         double maxLike = 0.0;
      |                ^~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c em_meta_bc.cpp -o em_meta_bc.o
em_meta_bc.cpp: In member function ‘double em_meta::bc_et_step()’:
em_meta_bc.cpp:237:16: warning: variable ‘maxLike’ set but not used [-Wunused-but-set-variable]
  237 |         double maxLike = 0.0;
      |                ^~~~~~~
em_meta_bc.cpp: In member function ‘double em_meta::bc_fixedN_et_step()’:
em_meta_bc.cpp:523:16: warning: variable ‘maxLike’ set but not used [-Wunused-but-set-variable]
  523 |         double maxLike = 0.0;
      |                ^~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c em_mvn.cpp -o em_mvn.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c em_mvt.cpp -o em_mvt.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c em_mvt2.cpp -o em_mvt2.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hc_meta.cpp -o hc_meta.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c immunoClust.c -o immunoClust.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c meta_norm.cpp -o meta_norm.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c meta_scale.cpp -o meta_scale.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c normalize.cpp -o normalize.o
normalize.cpp: In member function ‘int normalize::scale_X(int, int)’:
normalize.cpp:272:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  272 |     if( L < COEFF )
      |     ^~
normalize.cpp:275:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  275 |  int k, j, p;
      |  ^~~
normalize.cpp: In member function ‘int normalize::linear_Y(int, int)’:
normalize.cpp:377:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  377 |     if( L < COEFF )
      |     ^~
normalize.cpp:380:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  380 |  int k, j, p;
      |  ^~~
normalize.cpp: In member function ‘int normalize::scale_Y(int, int)’:
normalize.cpp:458:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  458 |     if( L < COEFF )
      |     ^~
normalize.cpp:461:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  461 |  int k, j, p;
      |  ^~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sub_mvn.cpp -o sub_mvn.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c util.cpp -o util.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vs_htrans.cpp -o vs_htrans.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-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_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 10 ]
> 
> proc.time()
   user  system elapsed 
  4.307   0.182   4.474 

Example timings

immunoClust.Rcheck/immunoClust-Ex.timings

nameusersystemelapsed
bhattacharyya0.0110.0040.015
cell.ClustData0.8910.0080.900
cell.EM0.6210.0030.624
cell.FitModel0.5810.0010.581
cell.ME0.3970.0000.396
cell.SubClustering13.013 0.19113.205
cell.hclust0.0060.0010.006
cell.process81.659 0.04381.705
cell.removed0.0090.0000.010
dat.exp0.7260.0020.728
dat.fcs88.600 0.00988.610
dat.meta0.0040.0000.004
immunoClust.methods0.0020.0000.002
immunoClust.object0.0040.0000.004
immunoMeta.methods0.0020.0020.003
immunoMeta.object0.0080.0020.011
meta.ME0.0170.0000.017
meta.SubClustering0.0880.0000.088
meta.clustering0.8150.0000.815
meta.export0.7620.0000.762
meta.exprs0.0080.0000.008
meta.hclust0.0040.0000.003
meta.normalize0.0020.0000.002
meta.process0.7390.0160.755
meta.regnorm0.0010.0030.005
plot.immunoClust0.5690.0120.581
plot.immunoMeta1.5240.0121.536
splom.immunoClust1.0360.0001.036
trans.ApplyToData0.0410.0000.041
trans.FitToData0.160.000.16