Multiple platform build/check report for BioC 3.14 - CHECK results for lipidr on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: lipidr

Version: 2.8.1

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lipidr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings lipidr_2.8.1.tar.gz

StartedAt: 2022-04-12 22:01:33 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 22:12:04 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 631.3 seconds

RetCode: 0

Status: OK

CheckDir: lipidr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lipidr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings lipidr_2.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/lipidr.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lipidr/DESCRIPTION' ... OK
* this is package 'lipidr' version '2.8.1'
* 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 whether package 'lipidr' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
lsea 2.64   0.08   11.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
lsea 2.47   0.09   12.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'spelling.R'
  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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/lipidr_2.8.1.tar.gz && rm -rf lipidr.buildbin-libdir && mkdir lipidr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lipidr.buildbin-libdir lipidr_2.8.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL lipidr_2.8.1.zip && rm lipidr_2.8.1.tar.gz lipidr_2.8.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 17 1841k   17  317k    0     0   651k      0  0:00:02 --:--:--  0:00:02  651k
 96 1841k   96 1776k    0     0  1196k      0  0:00:01  0:00:01 --:--:-- 1195k
100 1841k  100 1841k    0     0  1209k      0  0:00:01  0:00:01 --:--:-- 1210k

install for i386

* installing *source* package 'lipidr' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lipidr'
    finding HTML links ... done
    LipidomicsExperiment-class              html  
    LipidomicsExperiment                    html  
    finding level-2 HTML links ... done

    add_sample_annotation                   html  
    annotate_lipids                         html  
    as_lipidomics_experiment                html  
    data_normalized                         html  
    de_analysis                             html  
    filter_by_cv                            html  
    gen_lipidsets                           html  
    impute_na                               html  
    lipidDefaults                           html  
    lipidnames_pattern                      html  
    lipidr-data                             html  
    lipidr-package                          html  
    lsea                                    html  
    mva                                     html  
    mw                                      html  
    non_parsed_molecules                    html  
    normalize_istd                          html  
    normalize_pqn                           html  
    pipe                                    html  
    plot_chain_distribution                 html  
    plot_heatmap                            html  
    plot_lipidclass                         html  
    plot_molecules                          html  
    plot_samples                            html  
    plot_trend                              html  
    read_skyline                            html  
    remove_non_parsed_molecules             html  
    set_attr                                html  
    summarize_transitions                   html  
    update_molecule_names                   html  
    use_interactive_graphics                html  
*** copying figures
** 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

install for x64

* installing *source* package 'lipidr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lipidr' as lipidr_2.8.1.zip
* DONE (lipidr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'lipidr' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+   spelling::spell_check_test(
+     vignettes = TRUE, error = FALSE,
+     skip_on_cran = TRUE
+   )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
   0.23    0.04    0.26


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+   spelling::spell_check_test(
+     vignettes = TRUE, error = FALSE,
+     skip_on_cran = TRUE
+   )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
   0.28    0.06    0.32


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)
> library(lipidr)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

> test_check("lipidr")
[1] 18866.28
[ FAIL 0 | WARN 3 | SKIP 15 | PASS 370 ]

== Skipped tests ===============================================================
* On Bioconductor (12)
* empty test (3)

[ FAIL 0 | WARN 3 | SKIP 15 | PASS 370 ]
> 
> proc.time()
   user  system elapsed 
  54.73    1.62  164.76


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
> library(lipidr)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

> test_check("lipidr")
[1] 18866.28
[ FAIL 0 | WARN 3 | SKIP 15 | PASS 370 ]

== Skipped tests ===============================================================
* On Bioconductor (12)
* empty test (3)

[ FAIL 0 | WARN 3 | SKIP 15 | PASS 370 ]
> 
> proc.time()
   user  system elapsed 
  55.32    0.87  165.67

name	user	system	elapsed
add_sample_annotation	1.13	0.08	1.38
annotate_lipids	0.14	0.00	0.14
data_normalized	0.04	0.04	0.09
de_analysis	0.65	0.05	0.69
filter_by_cv	0.10	0.00	0.11
gen_lipidsets	0.16	0.02	0.17
impute_na	0.67	0.01	0.69
lipidDefaults	0.02	0.02	0.03
lipidnames_pattern	0	0	0
lipidr-data	0.03	0.03	0.06
lsea	2.64	0.08	11.78
mva	2.78	0.04	2.83
mw	0	0	0
non_parsed_molecules	0.06	0.00	0.06
normalize_istd	0.87	0.02	0.89
normalize_pqn	0.83	0.00	0.83
pipe	0.10	0.00	0.09
plot_chain_distribution	0.73	0.01	0.75
plot_heatmap	3.52	0.05	4.47
plot_lipidclass	2.54	0.06	2.67
plot_molecules	4.32	0.00	4.32
plot_samples	1.54	0.10	1.64
plot_trend	0.36	0.01	0.37
read_skyline	0.50	0.02	0.52
remove_non_parsed_molecules	0.08	0.01	0.09
set_attr	0.08	0.00	0.08
summarize_transitions	0.62	0.02	0.64
update_molecule_names	0.21	0.05	0.25
use_interactive_graphics	0.12	0.01	0.14

name	user	system	elapsed
add_sample_annotation	0.75	0.03	0.79
annotate_lipids	0.13	0.00	0.12
data_normalized	0.04	0.01	0.04
de_analysis	0.57	0.03	0.61
filter_by_cv	0.1	0.0	0.1
gen_lipidsets	0.23	0.00	0.23
impute_na	0.67	0.05	0.72
lipidDefaults	0.00	0.02	0.01
lipidnames_pattern	0	0	0
lipidr-data	0.05	0.00	0.05
lsea	2.47	0.09	12.92
mva	3.07	0.03	3.11
mw	0	0	0
non_parsed_molecules	0.03	0.03	0.06
normalize_istd	1.25	0.03	1.28
normalize_pqn	1.02	0.00	1.02
pipe	0.14	0.03	0.17
plot_chain_distribution	1.11	0.04	1.14
plot_heatmap	4.06	0.09	4.16
plot_lipidclass	2.21	0.05	2.25
plot_molecules	4.12	0.02	4.14
plot_samples	1.92	0.00	1.92
plot_trend	0.44	0.00	0.44
read_skyline	0.55	0.00	0.55
remove_non_parsed_molecules	0.08	0.00	0.08
set_attr	0.04	0.03	0.08
summarize_transitions	0.69	0.01	0.70
update_molecule_names	0.28	0.02	0.30
use_interactive_graphics	0.08	0.05	0.12

CHECK results for lipidr on tokay2

Summary

Command output

Installation output

Tests output

Example timings