Package: ropls

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ropls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ropls_1.12.0.tar.gz

StartedAt: 2018-10-16 23:47:45 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:49:02 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 77.1 seconds

RetCode: 0

Status:  OK

CheckDir: ropls.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ropls.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ropls_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ropls.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ropls/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ropls’ version ‘1.12.0’
* 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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ropls’ ...
** 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
* DONE (ropls)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> BiocGenerics:::testPackage("ropls")
OPLS-DA
10 samples x 8 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum)  RMSEE RMSEP pre ort
Total    0.699    0.976    0.94 0.0928 0.244   1   1
PLS-DA
10 samples x 8 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum)  RMSEE  RMSEP pre ort
Total    0.753     0.99   0.937 0.0636 0.0537   3   0
dev.new(): using pdf(file="Rplots1.pdf")
PLS-DA
47 samples x 109 variables and 1 response
standard scaling of predictors and response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.211     0.47  0.0394 0.338   2   0 0.05 0.05
dev.new(): using pdf(file="Rplots2.pdf")
PLS-DA
47 samples x 109 variables and 1 response
pareto scaling of predictors and standard scaling of response(s)
      R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y  pQ2
Total    0.204    0.442  0.0531 0.353   2   0  0.2 0.05
dev.new(): using pdf(file="Rplots3.pdf")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
dev.new(): using pdf(file="Rplots6.pdf")
dev.new(): using pdf(file="Rplots7.pdf")
dev.new(): using pdf(file="Rplots8.pdf")
dev.new(): using pdf(file="Rplots9.pdf")
dev.new(): using pdf(file="Rplots10.pdf")
dev.new(): using pdf(file="Rplots11.pdf")
dev.new(): using pdf(file="Rplots12.pdf")
dev.new(): using pdf(file="Rplots13.pdf")
dev.new(): using pdf(file="Rplots14.pdf")
dev.new(): using pdf(file="Rplots15.pdf")
dev.new(): using pdf(file="Rplots16.pdf")
dev.new(): using pdf(file="Rplots17.pdf")

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
     1    2 ...  999 1000
1 TRUE TRUE ... TRUE TRUE
     dim  class      mode    typeof size NAs
 10 x 10 matrix character character 0 Mb   0
      1   2 ...   9  10
1     a   a ...   a   a
2     a   a ...   a   a
... ... ... ... ... ...
9     a   a ...   a   a
10    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


RUNIT TEST PROTOCOL -- Tue Oct 16 23:48:55 2018 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ropls RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: 'permI' set to 0 because train/test partition is selected 
2: 'permI' set to 0 because train/test partition is selected 
3: Character 'parAsColFcVn' set to a factor 
> 
> proc.time()
   user  system elapsed 
 10.486   0.543  11.035 

name	user	system	elapsed
checkW4M	0.190	0.022	0.213
coef	1.157	0.162	1.332
fitted	1.737	0.153	1.901
fromW4M	0.177	0.001	0.180
getLoadingMN	1.063	0.139	1.205
getPcaVarVn	0.135	0.010	0.147
getScoreMN	1.071	0.142	1.219
getSubsetVi	0.092	0.011	0.104
getSummaryDF	1.090	0.127	1.222
getVipVn	1.005	0.127	1.135
getWeightMN	1.016	0.133	1.154
opls-class	2.971	0.258	3.240
opls	2.687	0.230	2.925
plot	1.247	0.137	1.388
predict	0.102	0.012	0.114
print	1.007	0.130	1.142
residuals	0.746	0.062	0.810
ropls-package	2.134	0.236	2.379
show	0.978	0.124	1.106
strF	0.019	0.002	0.022
tested	0.111	0.009	0.121
toW4M	0.172	0.004	0.176