Multiple platform build/check report for BioC 3.12 - CHECK report for lipidr on tokay1

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CHECK report for lipidr on tokay1

This page was generated on 2021-05-06 12:31:57 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the lipidr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.

lipidr 2.4.0 (landing page)
Ahmed Mohamed

Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)

URL: https://git.bioconductor.org/packages/lipidr

Branch: RELEASE_3_12

Last Commit: fcfbe01

Last Changed Date: 2020-10-27 11:45:29 -0400 (Tue, 27 Oct 2020)

malbec1

Linux (Ubuntu 18.04.5 LTS) / x86_64

tokay1

Windows Server 2012 R2 Standard / x64

merida1

macOS 10.14.6 Mojave / x86_64

Summary

Package: lipidr

Version: 2.4.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lipidr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings lipidr_2.4.0.tar.gz

StartedAt: 2021-05-06 04:08:12 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:21:52 -0400 (Thu, 06 May 2021)

EllapsedTime: 819.7 seconds

RetCode: 0

Status: OK

CheckDir: lipidr.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lipidr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings lipidr_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/lipidr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.4.0'
* 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 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
** running examples for arch 'x64' ... OK
* 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

Installation output

lipidr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/lipidr_2.4.0.tar.gz && rm -rf lipidr.buildbin-libdir && mkdir lipidr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lipidr.buildbin-libdir lipidr_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL lipidr_2.4.0.zip && rm lipidr_2.4.0.tar.gz lipidr_2.4.0.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
100 1857k  100 1857k    0     0  28.3M      0 --:--:-- --:--:-- --:--:-- 28.7M

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_2.4.0.zip
* DONE (lipidr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'lipidr' successfully unpacked and MD5 sums checked

Tests output

lipidr.Rcheck/tests_i386/spelling.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 
   0.25    0.04    0.28

lipidr.Rcheck/tests_x64/spelling.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 
   0.18    0.00    0.17

lipidr.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
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, 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 object is masked from 'package:base':

    expand.grid

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

[ FAIL 0 | WARN 15 | SKIP 15 | PASS 369 ]
> 
> proc.time()
   user  system elapsed 
  48.04    1.37  255.09

lipidr.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
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, 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 object is masked from 'package:base':

    expand.grid

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

[ FAIL 0 | WARN 15 | SKIP 15 | PASS 369 ]
> 
> proc.time()
   user  system elapsed 
  52.95    0.50  248.34

Example timings

lipidr.Rcheck/examples_i386/lipidr-Ex.timings

name	user	system	elapsed
add_sample_annotation	0.72	0.02	1.94
annotate_lipids	0.14	0.00	0.14
data_normalized	0.05	0.01	0.07
de_analysis	0.50	0.02	0.51
filter_by_cv	0.11	0.00	0.11
gen_lipidsets	0.11	0.04	0.16
impute_na	0.78	0.04	0.81
lipidDefaults	0.00	0.01	0.02
lipidnames_pattern	0.00	0.02	0.01
lipidr-data	0.03	0.03	0.06
lsea	1.50	0.06	1.57
mva	2.49	0.02	2.50
mw	0	0	0
non_parsed_molecules	0.06	0.00	0.06
normalize_istd	0.78	0.01	0.80
normalize_pqn	0.70	0.02	0.71
pipe	0.08	0.00	0.08
plot_chain_distribution	0.67	0.01	0.69
plot_heatmap	2.84	0.05	3.75
plot_lipidclass	2.49	0.03	2.51
plot_molecules	3.44	0.00	3.44
plot_samples	1.53	0.05	1.58
plot_trend	0.36	0.01	0.37
read_skyline	0.39	0.00	0.39
remove_non_parsed_molecules	0.06	0.02	0.08
set_attr	0.05	0.02	0.06
summarize_transitions	0.48	0.00	0.48
update_molecule_names	0.16	0.00	0.16
use_interactive_graphics	0.07	0.05	0.12

lipidr.Rcheck/examples_x64/lipidr-Ex.timings

name	user	system	elapsed
add_sample_annotation	1.05	0.03	1.08
annotate_lipids	0.27	0.00	0.27
data_normalized	0.05	0.02	0.06
de_analysis	0.79	0.03	0.83
filter_by_cv	0.11	0.00	0.11
gen_lipidsets	0.19	0.02	0.20
impute_na	1.16	0.03	1.18
lipidDefaults	0.00	0.03	0.03
lipidnames_pattern	0.00	0.01	0.02
lipidr-data	0.06	0.02	0.08
lsea	1.80	0.03	1.83
mva	2.45	0.03	2.48
mw	0	0	0
non_parsed_molecules	0.07	0.02	0.08
normalize_istd	0.82	0.00	0.83
normalize_pqn	0.83	0.00	0.83
pipe	0.08	0.00	0.07
plot_chain_distribution	0.73	0.01	0.75
plot_heatmap	3.33	0.02	3.47
plot_lipidclass	2.47	0.03	2.50
plot_molecules	4.16	0.02	4.17
plot_samples	1.79	0.01	1.82
plot_trend	0.38	0.03	0.40
read_skyline	0.44	0.00	0.44
remove_non_parsed_molecules	0.06	0.03	0.09
set_attr	0.06	0.00	0.07
summarize_transitions	0.63	0.00	0.62
update_molecule_names	0.29	0.00	0.30
use_interactive_graphics	0.18	0.02	0.19