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This page was generated on 2024-03-04 11:39:50 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1776/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ropls 1.35.4  (landing page)
Etienne A. Thevenot
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/ropls
git_branch: devel
git_last_commit: 35e1b2d
git_last_commit_date: 2023-12-06 10:05:27 -0500 (Wed, 06 Dec 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for ropls on merida1


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.

raw results


Summary

Package: ropls
Version: 1.35.4
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_1.35.4.tar.gz
StartedAt: 2024-03-02 09:46:27 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 09:55:57 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 569.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ropls.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.35.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ropls.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 ‘1.35.4’
* 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’
.gg_scoreplot: no visible binding for global variable ‘.data’
.gg_scoreplot: no visible binding for global variable ‘.text’
Undefined global functions or variables:
  .comp1 .comp2 .data .text
* 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         13.515  0.377  17.905
gg_scoreplot 11.739  0.702  24.875
plot          6.466  0.234   9.270
opls-class    4.259  0.172   6.256
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/ropls.Rcheck/00check.log’
for details.



Installation output

ropls.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ropls
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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)

Tests output

ropls.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 40.017   1.808  50.024 

Example timings

ropls.Rcheck/ropls-Ex.timings

nameusersystemelapsed
checkW4M0.3680.0230.525
coef1.2530.0701.717
fitted1.6110.0632.232
fromW4M0.2550.0070.334
getEset1.1760.0501.623
getLoadingMN1.6690.0752.270
getMset0.6990.0130.910
getOpls1.6470.0562.157
getPcaVarVn0.1540.0070.190
getScoreMN1.1120.0641.541
getSubsetVi0.1220.0080.170
getSummaryDF1.1050.0541.864
getVipVn1.0770.0541.472
getWeightMN1.0850.0751.282
gg_scoreplot11.739 0.70224.875
opls-class4.2590.1726.256
opls13.515 0.37717.905
oplsMultiDataSet-class0.0000.0000.001
plot6.4660.2349.270
predict0.1270.0130.235
print1.1490.0621.687
residuals0.8270.0331.149
show1.1510.0561.760
tested0.1210.0120.210
toW4M0.2300.0170.378
view0.8370.1731.802