| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:43 -0400 (Fri, 15 Oct 2021).
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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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 915/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| immunoClust 1.24.0 (landing page) Till Soerensen
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: immunoClust |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings immunoClust_1.24.0.tar.gz |
| StartedAt: 2021-10-14 10:15:29 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 10:20:08 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 279.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: immunoClust.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:immunoClust.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings immunoClust_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/immunoClust.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.24.0’
* 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
cell.process 95.979 0.408 96.392
dat.fcs 91.169 0.024 91.196
cell.SubClustering 16.313 0.052 16.368
* 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-3.13-bioc/meat/immunoClust.Rcheck/00check.log’
for details.
immunoClust.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL immunoClust
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* installing to library ‘/home/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)
immunoClust.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
4.460 0.220 4.666
immunoClust.Rcheck/immunoClust-Ex.timings
| name | user | system | elapsed | |
| bhattacharyya | 0.042 | 0.000 | 0.042 | |
| cell.ClustData | 1.026 | 0.011 | 1.040 | |
| cell.EM | 0.643 | 0.016 | 0.659 | |
| cell.FitModel | 0.602 | 0.000 | 0.603 | |
| cell.ME | 0.417 | 0.000 | 0.416 | |
| cell.SubClustering | 16.313 | 0.052 | 16.368 | |
| cell.hclust | 0.003 | 0.004 | 0.007 | |
| cell.process | 95.979 | 0.408 | 96.392 | |
| cell.removed | 0.010 | 0.004 | 0.014 | |
| dat.exp | 0.757 | 0.012 | 0.769 | |
| dat.fcs | 91.169 | 0.024 | 91.196 | |
| dat.meta | 0.005 | 0.000 | 0.005 | |
| immunoClust.methods | 0.000 | 0.004 | 0.003 | |
| immunoClust.object | 0.001 | 0.004 | 0.006 | |
| immunoMeta.methods | 0.004 | 0.000 | 0.005 | |
| immunoMeta.object | 0.002 | 0.012 | 0.014 | |
| meta.ME | 0.017 | 0.000 | 0.017 | |
| meta.SubClustering | 0.090 | 0.000 | 0.091 | |
| meta.clustering | 0.910 | 0.000 | 0.911 | |
| meta.export | 0.796 | 0.000 | 0.797 | |
| meta.exprs | 0.008 | 0.000 | 0.009 | |
| meta.hclust | 0.004 | 0.000 | 0.004 | |
| meta.normalize | 0.003 | 0.000 | 0.003 | |
| meta.process | 0.796 | 0.004 | 0.800 | |
| meta.regnorm | 0.005 | 0.000 | 0.006 | |
| plot.immunoClust | 0.587 | 0.012 | 0.598 | |
| plot.immunoMeta | 2.138 | 0.028 | 2.166 | |
| splom.immunoClust | 1.238 | 0.012 | 1.250 | |
| trans.ApplyToData | 0.049 | 0.000 | 0.050 | |
| trans.FitToData | 0.158 | 0.004 | 0.162 | |