Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:19 -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: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ropls.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ropls_1.34.0.tar.gz |
StartedAt: 2024-04-16 03:13:01 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 03:17:43 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 281.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ropls.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ropls.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ropls_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ropls.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 5.89 0.148 6.038 * 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 ... ‘ropls-vignette.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/ropls.Rcheck/00check.log’ for details.
ropls.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ropls ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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-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) > 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 18.763 0.648 19.397
ropls.Rcheck/ropls-Ex.timings
name | user | system | elapsed | |
checkW4M | 0.122 | 0.008 | 0.131 | |
coef | 0.580 | 0.012 | 0.592 | |
fitted | 0.699 | 0.004 | 0.703 | |
fromW4M | 0.108 | 0.000 | 0.108 | |
getEset | 1.089 | 0.036 | 1.126 | |
getLoadingMN | 0.510 | 0.004 | 0.514 | |
getMset | 0.288 | 0.000 | 0.288 | |
getOpls | 0.766 | 0.020 | 0.787 | |
getPcaVarVn | 0.079 | 0.000 | 0.079 | |
getScoreMN | 0.512 | 0.001 | 0.515 | |
getSubsetVi | 0.055 | 0.002 | 0.057 | |
getSummaryDF | 0.513 | 0.012 | 0.525 | |
getVipVn | 0.509 | 0.004 | 0.514 | |
getWeightMN | 0.540 | 0.004 | 0.544 | |
gg_scoreplot | 3.925 | 0.152 | 4.077 | |
opls-class | 2.246 | 0.116 | 2.361 | |
opls | 5.890 | 0.148 | 6.038 | |
oplsMultiDataSet-class | 0 | 0 | 0 | |
plot | 2.730 | 0.044 | 2.774 | |
predict | 0.067 | 0.004 | 0.071 | |
0.548 | 0.000 | 0.548 | ||
residuals | 0.369 | 0.000 | 0.368 | |
show | 0.570 | 0.024 | 0.594 | |
tested | 0.056 | 0.008 | 0.064 | |
toW4M | 0.113 | 0.000 | 0.113 | |
view | 0.498 | 0.015 | 0.515 | |