| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:21:40 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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. |
| Package 951/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| immunoClust 1.28.0 (landing page) Till Soerensen
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: immunoClust |
| Version: 1.28.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunoClust.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings immunoClust_1.28.0.tar.gz |
| StartedAt: 2022-10-19 01:07:59 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 01:12:39 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 280.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: immunoClust.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunoClust.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings immunoClust_1.28.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/immunoClust.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.28.0'
* 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
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/immunoClust/libs/x64/immunoClust.dll':
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. 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
dat.fcs 81.57 0.24 81.81
cell.process 74.34 0.24 74.58
cell.SubClustering 16.79 0.09 16.87
* 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
'F:/biocbuild/bbs-3.15-bioc/meat/immunoClust.Rcheck/00check.log'
for details.
immunoClust.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL immunoClust
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'immunoClust' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_meta.cpp -o R_meta.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_model.cpp -o R_model.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dist_mvn.cpp -o dist_mvn.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/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 '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++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/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++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_mvn.cpp -o em_mvn.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_mvt.cpp -o em_mvt.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c em_mvt2.cpp -o em_mvt2.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hc_meta.cpp -o hc_meta.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/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-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c immunoClust.c -o immunoClust.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c meta_norm.cpp -o meta_norm.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c meta_scale.cpp -o meta_scale.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sub_mvn.cpp -o sub_mvn.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vs_htrans.cpp -o vs_htrans.o
g++ -std=gnu++11 -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_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 13 ]
>
> proc.time()
user system elapsed
6.78 0.29 7.12
immunoClust.Rcheck/immunoClust-Ex.timings
| name | user | system | elapsed | |
| bhattacharyya | 0.03 | 0.00 | 0.03 | |
| cell.ClustData | 1.72 | 0.00 | 1.77 | |
| cell.EM | 1.04 | 0.03 | 1.07 | |
| cell.FitModel | 0.94 | 0.00 | 0.97 | |
| cell.ME | 0.67 | 0.00 | 0.67 | |
| cell.SubClustering | 16.79 | 0.09 | 16.87 | |
| cell.hclust | 0.01 | 0.00 | 0.02 | |
| cell.process | 74.34 | 0.24 | 74.58 | |
| cell.removed | 0.02 | 0.00 | 0.01 | |
| dat.exp | 0.86 | 0.03 | 0.89 | |
| dat.fcs | 81.57 | 0.24 | 81.81 | |
| dat.meta | 0.00 | 0.00 | 0.01 | |
| immunoClust.methods | 0.00 | 0.01 | 0.02 | |
| immunoClust.object | 0.02 | 0.00 | 0.02 | |
| immunoMeta.methods | 0 | 0 | 0 | |
| immunoMeta.object | 0.02 | 0.00 | 0.02 | |
| meta.ME | 0.00 | 0.03 | 0.03 | |
| meta.SubClustering | 0.14 | 0.02 | 0.15 | |
| meta.clustering | 1.14 | 0.00 | 1.14 | |
| meta.export | 0.85 | 0.00 | 0.85 | |
| meta.exprs | 0.00 | 0.02 | 0.01 | |
| meta.hclust | 0 | 0 | 0 | |
| meta.normalize | 0 | 0 | 0 | |
| meta.process | 1.25 | 0.00 | 1.25 | |
| meta.regnorm | 0.02 | 0.00 | 0.02 | |
| plot.immunoClust | 0.62 | 0.01 | 0.64 | |
| plot.immunoMeta | 1.63 | 0.04 | 1.67 | |
| splom.immunoClust | 1.15 | 0.02 | 1.18 | |
| trans.ApplyToData | 0.03 | 0.02 | 0.04 | |
| trans.FitToData | 0.25 | 0.01 | 0.27 | |