Etienne A. Thevenot
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/ropls |
| git_branch: RELEASE_3_18 |
| git_last_commit: 415d359 |
| git_last_commit_date: 2023-10-24 10:44:19 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:38:10 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1791/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ropls 1.34.0 (landing page) Etienne A. Thevenot
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the ropls package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ropls.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. |
| Package: ropls |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ropls.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ropls_1.34.0.tar.gz |
| StartedAt: 2024-04-16 08:04:46 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 08:13:18 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 512.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ropls.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ropls.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ropls_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ropls.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ropls/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ropls’ version ‘1.34.0’
* 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 ‘ropls’ 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 ... NOTE
.gg_scoreplot: no visible binding for global variable ‘.comp1’
.gg_scoreplot: no visible binding for global variable ‘.comp2’
Undefined global functions or variables:
.comp1 .comp2
* 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
opls 14.264 0.305 15.532
gg_scoreplot 8.717 0.424 9.742
plot 6.662 0.151 7.018
opls-class 4.692 0.144 5.298
* 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
‘/Users/biocbuild/bbs-3.18-bioc/meat/ropls.Rcheck/00check.log’
for details.
ropls.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ropls ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘ropls’ ... ** 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 (ropls)
ropls.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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("ropls")
Loading required package: ropls
1) Data set:
183 samples x 109 variables
0 (0%) NAs
0 excluded variables (near zero variance)
standard x scaling
Summary of the 3 increasing variance spaced raw variables:
Citric acid Ortho-Hydroxyphenylacetic acid Acetaminophen glucuronide
Min. :3.978 Min. :3.516 Min. :-0.30001
1st Qu.:4.240 1st Qu.:4.260 1st Qu.: 0.04682
Median :4.354 Median :4.465 Median : 1.23248
Mean :4.352 Mean :4.438 Mean : 1.38781
3rd Qu.:4.450 3rd Qu.:4.656 3rd Qu.: 2.09594
Max. :4.804 Max. :5.428 Max. : 5.56739
2) Model: PCA
Correlations between variables and first 2 components:
p1 p2 cor_p1 cor_p2
Salicylic acid -0.0069 NA -0.028 NA
N-Acetylleucine 0.0015 NA 0.006 NA
Chenodeoxycholic acid isomer 0.0075 NA 0.030 NA
Pyridylacetylglycine 0.1500 NA 0.590 NA
Dimethylguanosine 0.1700 NA 0.670 NA
4-Acetamidobutanoic acid isomer 2 0.1800 NA 0.730 NA
FMNH2 NA -0.17 NA -0.56
Testosterone glucuronide NA -0.16 NA -0.54
6-(carboxymethoxy)-hexanoic acid NA -0.16 NA -0.52
Pyrocatechol sulfate NA 0.22 NA 0.72
Fumaric acid NA 0.22 NA 0.74
Pentose NA 0.24 NA 0.79
R2X R2X(cum) Iter.
p1 0.149 0.149 0
p2 0.103 0.252 0
1) Data set:
183 samples x 109 variables and 1 response
0 (0%) NAs
0 excluded variables (near zero variance)
standard x and y scaling
Summary of the 3 increasing variance spaced raw variables:
Citric acid Ortho-Hydroxyphenylacetic acid Acetaminophen glucuronide
Min. :3.978 Min. :3.516 Min. :-0.30001
1st Qu.:4.240 1st Qu.:4.260 1st Qu.: 0.04682
Median :4.354 Median :4.465 Median : 1.23248
Mean :4.352 Mean :4.438 Mean : 1.38781
3rd Qu.:4.450 3rd Qu.:4.656 3rd Qu.: 2.09594
Max. :4.804 Max. :5.428 Max. : 5.56739
2) Model: PLS-DA
Correlations between variables and first 2 components:
p1 p2 cor_p1 cor_p2
Testosterone glucuronide -0.180 NA -0.50 NA
6-(carboxymethoxy)-hexanoic acid -0.097 NA -0.27 NA
Asp-Leu/Ile isomer 1 -0.080 NA -0.22 NA
Glucuronic acid and/or isomers 0.220 NA 0.62 NA
Phe-Tyr-Asp (and isomers) 0.220 NA 0.63 NA
alpha-N-Phenylacetyl-glutamine 0.220 NA 0.64 NA
Porphobilinogen NA -0.200 NA -0.530
1-Methyluric acid NA -0.200 NA -0.530
p-Hydroxymandelic acid NA -0.200 NA -0.520
Malic acid NA 0.030 NA 0.078
p-Anisic acid NA 0.066 NA 0.180
Acetaminophen glucuronide NA 0.093 NA 0.240
R2X R2X(cum) R2Y R2Y(cum) Q2 Q2(cum) Signif. Iter.
p1 0.0984 0.0984 0.479 0.479 0.401 0.401 R1 1
p2 0.0861 0.1850 0.189 0.668 0.256 0.555 R1 1
Country Gr_Coffe ... Yoghurt Crisp_Brea
factor numeric ... numeric numeric
nRow nCol size NAs
16 21 0 Mb 3
Country Gr_Coffe ... Yoghurt Crisp_Brea
1 Ger 90 ... 30 26
2 Ita 82 ... 5 18
... ... ... ... ... ...
15 Spa 70 ... 16 13
16 Ire 30 ... 3 9
Country Gr_Coffe Inst_Coffe ... Olive_Oil Yoghurt Crisp_Brea
factor numeric numeric ... numeric numeric numeric
nRow nCol size NAs
16 21 0 Mb 3
Country Gr_Coffe Inst_Coffe ... Olive_Oil Yoghurt Crisp_Brea
1 Ger 90 49 ... 74 30 26
2 Ita 82 10 ... 94 5 18
3 Fra 88 42 ... 36 57 3
... ... ... ... ... ... ... ...
14 Fin 98 12 ... 17 <NA> 64
15 Spa 70 40 ... 91 16 13
16 Ire 30 52 ... 31 3 9
dim class mode typeof size NAs
1 x 1'000 matrix logical logical 0 Mb 0
V1 V2 ... V4 V5
1 TRUE TRUE ... TRUE TRUE
dim class mode typeof size NAs
10 x 10 matrix character character 0 Mb 0
V1 V2 ... V4 V5
1 a a ... a a
2 a a ... a a
... ... ... ... ... ...
4 a a ... a a
5 a a ... a a
dim class mode typeof size NAs min mean median max
183 x 109 matrix numeric double 0.2 Mb 0 -0.3 4.2 4.3 6
(2-methoxyethoxy)propanoic acid isomer (gamma)Glu-Leu/Ile ...
HU_011 3.019766011 3.888479324 ...
HU_014 3.81433889 4.277148905 ...
... ... ... ...
HU_208 3.748127215 4.523763202 ...
HU_209 4.208859398 4.675880567 ...
Valerylglycine isomer 2 Xanthosine
HU_011 3.889078716 4.075879575
HU_014 4.181765852 4.195761901
... ... ...
HU_208 4.634338821 4.487781609
HU_209 4.47194762 4.222953354
age bmi gender
numeric numeric factor
nRow nCol size NAs
183 3 0 Mb 0
age bmi gender
HU_011 29 19.75 M
HU_014 59 22.64 F
... ... ... ...
HU_208 27 18.61 F
HU_209 17.5 21.48 F
[ FAIL 0 | WARN 3 | SKIP 4 | PASS 61 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• empty test (4): 'test_opls.R:557:1', 'test_opls.R:595:1',
'test_opls.R:632:1', 'test_opls.R:639:1'
[ FAIL 0 | WARN 3 | SKIP 4 | PASS 61 ]
>
> proc.time()
user system elapsed
41.835 1.570 46.463
ropls.Rcheck/ropls-Ex.timings
| name | user | system | elapsed | |
| checkW4M | 0.293 | 0.014 | 0.364 | |
| coef | 1.298 | 0.077 | 1.581 | |
| fitted | 1.614 | 0.062 | 1.958 | |
| fromW4M | 0.249 | 0.011 | 0.301 | |
| getEset | 1.842 | 0.061 | 2.202 | |
| getLoadingMN | 1.114 | 0.058 | 1.382 | |
| getMset | 0.706 | 0.015 | 0.821 | |
| getOpls | 1.652 | 0.045 | 1.992 | |
| getPcaVarVn | 0.158 | 0.007 | 0.192 | |
| getScoreMN | 1.149 | 0.043 | 1.376 | |
| getSubsetVi | 0.137 | 0.010 | 0.174 | |
| getSummaryDF | 1.144 | 0.041 | 1.391 | |
| getVipVn | 1.126 | 0.043 | 1.351 | |
| getWeightMN | 1.144 | 0.040 | 1.367 | |
| gg_scoreplot | 8.717 | 0.424 | 9.742 | |
| opls-class | 4.692 | 0.144 | 5.298 | |
| opls | 14.264 | 0.305 | 15.532 | |
| oplsMultiDataSet-class | 0.000 | 0.001 | 0.001 | |
| plot | 6.662 | 0.151 | 7.018 | |
| predict | 0.125 | 0.006 | 0.135 | |
| 1.154 | 0.047 | 1.244 | ||
| residuals | 0.827 | 0.017 | 0.876 | |
| show | 1.165 | 0.045 | 1.236 | |
| tested | 0.126 | 0.007 | 0.136 | |
| toW4M | 0.236 | 0.009 | 0.261 | |
| view | 0.831 | 0.109 | 1.003 | |