| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 215/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biosigner 1.28.0 (landing page) Etienne A. Thevenot
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the biosigner package: - 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: biosigner |
| Version: 1.28.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biosigner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biosigner_1.28.0.tar.gz |
| StartedAt: 2023-10-17 05:59:34 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 06:06:28 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 414.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biosigner.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biosigner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biosigner_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biosigner.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biosigner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biosigner’ version ‘1.28.0’
* package encoding: UTF-8
* 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 ‘biosigner’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getMset 39.116 0.397 51.003
biosign 18.766 0.341 23.553
plot 8.040 0.112 10.547
biosign-class 4.066 0.100 5.821
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
y[4]: "0.8529397"
x[5]: "0.8908808"
y[5]: "0.9200604"
x[6]: "0.8449724"
y[6]: "0.8551306"
── Failure ('test_biosigner.R:252:3'): SummarizedExperiment ────────────────────
sac_accu.mn["AS", "randomforest"] not equivalent to 0.9200604.
1/1 mismatches
[1] 0.891 - 0.92 == -0.0292
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
* 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 ERROR
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biosigner.Rcheck/00check.log’
for details.
biosigner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biosigner ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘biosigner’ ... ** using staged installation ** R ** data ** inst ** 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 (biosigner)
biosigner.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
> test_check("biosigner")
Loading required package: biosigner
Selecting features for the plsda model
Significant features from 'S' groups:
plsda
m189.040t01.2 "S"
Accuracy:
plsda
Full 0.718
AS 0.711
S 0.697
Selecting features for the randomforest model
Significant features from 'S' groups:
randomforest
m427.215t07.9 "S"
Accuracy:
randomforest
Full 0.743
AS 0.714
S 0.665
Selecting features for the svm model
No significant variable found for the selected classifier(s): 'svm'
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
m189.040t01.2 "A" "S" "B"
m427.215t07.9 "A" "S" "B"
m539.231t06.6 "A" "S" "B"
m164.035t02.1 "A" "D" "S"
m557.311t10.9 "S" "C" "B"
m511.313t08.7 "E" "E" "S"
Accuracy:
plsda randomforest svm
Full 0.729 0.812 0.729
AS 0.792 0.917 0.583
S 0.708 0.750 0.583
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
m427.215t07.9 "A" "S" "B"
m189.040t01.2 "S" "B" "E"
Accuracy:
plsda randomforest svm
Full 0.718 0.743 0.688
AS 0.711 0.714 0.745
S 0.697 0.665 NA
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
p-Anisic acid "S" "S" "S"
Testosterone glucuronide "S" "S" "S"
Pantothenic acid "S" "A" "S"
Malic acid "S" "A" "A"
Oxoglutaric acid "E" "S" "S"
Glucuronic acid and/or isomers "B" "E" "S"
2-Isopropylmalic acid "E" "E" "S"
3,7-Dimethyluric acid "E" "E" "S"
4-Acetamidobutanoic acid isomer 3 "E" "E" "S"
N-Acetylleucine "E" "E" "S"
N2-Acetylaminoadipic acid "E" "E" "S"
N4-Acetylcytidine "E" "E" "S"
Pyrroledicarboxylic acid "E" "E" "S"
Taurine "E" "E" "S"
Xanthosine "E" "E" "S"
Accuracy:
plsda randomforest svm
Full 0.871 0.840 0.884
AS 0.883 0.891 0.927
S 0.877 0.845 0.931
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
m103.040t01.3 "S" "B" "B"
m103.040t01.6 "S" "B" "E"
m110.985t00.9 "S" "B" "E"
m116.072t01.0 "S" "B" "E"
m104.043t01.6 "S" "E" "E"
m117.055t02.8 "S" "E" "E"
Accuracy:
plsda randomforest svm
Full 0.690 0.606 0.68
AS 0.724 0.606 0.50
S 0.724 NA NA
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
p-Anisic acid "S" "S" "S"
Testosterone glucuronide "S" "S" "S"
Pantothenic acid "S" "A" "S"
Malic acid "S" "A" "A"
Oxoglutaric acid "E" "S" "S"
Glucuronic acid and/or isomers "B" "E" "S"
2-Isopropylmalic acid "E" "E" "S"
3,7-Dimethyluric acid "E" "E" "S"
4-Acetamidobutanoic acid isomer 3 "E" "E" "S"
N-Acetylleucine "E" "E" "S"
N2-Acetylaminoadipic acid "E" "E" "S"
N4-Acetylcytidine "E" "E" "S"
Pyrroledicarboxylic acid "E" "E" "S"
Taurine "E" "E" "S"
Xanthosine "E" "E" "S"
Accuracy:
plsda randomforest svm
Full 0.871 0.840 0.884
AS 0.883 0.891 0.927
S 0.877 0.845 0.931
Selecting the features for the 'agilent' dataset:
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
VEPH1 "S" "E" "B"
LHFP "S" "E" "B"
C10orf90 "B" "E" "S"
EZH2 "E" "S" "E"
Accuracy:
plsda randomforest svm
Full 1 1.000 1.000
AS 1 0.900 0.983
S 1 0.917 0.983
Selecting the features for the 'hgu95' dataset:
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
TSPAN4 "S" "S" "E"
TBC1D16 "S" "E" "B"
NASP "S" "E" "E"
Accuracy:
plsda randomforest svm
Full 1 1 1.000
AS 1 1 0.917
S 1 1 NA
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
m495.261t08.7 "A" "B" "S"
m497.284t08.1 "S" "S" "C"
m497.275t08.1 "S" "A" "E"
Accuracy:
plsda randomforest svm
Full 0.782 0.831 0.738
AS 0.760 0.808 0.708
S 0.823 0.739 0.708
Selecting the features for the 'agilent' dataset:
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
VEPH1 "S" "E" "B"
LHFP "S" "E" "B"
C10orf90 "B" "E" "S"
EZH2 "E" "S" "E"
Accuracy:
plsda randomforest svm
Full 1 1.000 1.000
AS 1 0.900 0.983
S 1 0.917 0.983
Selecting the features for the 'hgu95' dataset:
Selecting features for the plsda model
Selecting features for the randomforest model
Selecting features for the svm model
Significant features from 'S' groups:
plsda randomforest svm
TSPAN4 "S" "S" "E"
TBC1D16 "S" "E" "B"
NASP "S" "E" "E"
Accuracy:
plsda randomforest svm
Full 1 1 1.000
AS 1 1 0.917
S 1 1 NA
Selecting features for the plsda model
No significant variable found for the selected classifier(s): 'plsda'
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_biosigner.R:187:5'): biosign_sacurine ────────────────────────
`biosignMC` not identical to `accMC`.
3/9 mismatches
x[4]: "0.8397755"
y[4]: "0.8529397"
x[5]: "0.8908808"
y[5]: "0.9200604"
x[6]: "0.8449724"
y[6]: "0.8551306"
── Failure ('test_biosigner.R:252:3'): SummarizedExperiment ────────────────────
sac_accu.mn["AS", "randomforest"] not equivalent to 0.9200604.
1/1 mismatches
[1] 0.891 - 0.92 == -0.0292
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
biosigner.Rcheck/biosigner-Ex.timings
| name | user | system | elapsed | |
| biosign-class | 4.066 | 0.100 | 5.821 | |
| biosign | 18.766 | 0.341 | 23.553 | |
| biosignMultiDataSet-class | 0 | 0 | 0 | |
| getAccuracyMN | 3.032 | 0.054 | 3.982 | |
| getBiosign | 2.852 | 0.041 | 3.716 | |
| getEset | 3.134 | 0.044 | 4.110 | |
| getMset | 39.116 | 0.397 | 51.003 | |
| getSignatureLs | 3.116 | 0.050 | 4.079 | |
| plot | 8.040 | 0.112 | 10.547 | |
| predict | 3.017 | 0.050 | 3.966 | |
| show | 3.501 | 0.065 | 4.593 | |