Ahmed Mohamed
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/lipidr |
| Branch: RELEASE_3_11 |
| Last Commit: b743db2 |
| Last Changed Date: 2020-04-27 15:26:15 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:02 -0400 (Sat, 17 Oct 2020).
| 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. |
| Package 943/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| lipidr 2.2.0 Ahmed Mohamed
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: lipidr |
| Version: 2.2.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:lipidr.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings lipidr_2.2.0.tar.gz |
| StartedAt: 2020-10-17 02:39:21 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:43:44 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 262.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: lipidr.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:lipidr.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings lipidr_2.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/lipidr.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lipidr/DESCRIPTION’ ... OK
* this is package ‘lipidr’ version ‘2.2.0’
* 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 ‘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
* 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
plot_class_enrichment: no visible binding for global variable
‘Significant’
Undefined global functions or variables:
Significant
* 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
plot_heatmap 5.204 0.032 5.479
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 1 NOTE
See
‘/home/biocbuild/bbs-3.11-bioc/meat/lipidr.Rcheck/00check.log’
for details.
lipidr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL lipidr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘lipidr’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** 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 * DONE (lipidr)
lipidr.Rcheck/tests/spelling.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> if (requireNamespace("spelling", quietly = TRUE)) {
+ spelling::spell_check_test(
+ vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE
+ )
+ }
NULL
>
> proc.time()
user system elapsed
0.260 0.042 0.339
lipidr.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
> library(lipidr)
Loading required package: SummarizedExperiment
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, 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
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
> test_check("lipidr")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 353 | SKIPPED: 16 | WARNINGS: 15 | FAILED: 0 ]
>
> proc.time()
user system elapsed
40.635 3.665 41.044
lipidr.Rcheck/lipidr-Ex.timings
| name | user | system | elapsed | |
| add_sample_annotation | 0.961 | 0.020 | 1.121 | |
| annotate_lipids | 0.214 | 0.000 | 0.213 | |
| data_normalized | 0.104 | 0.020 | 0.124 | |
| de_analysis | 1.544 | 0.064 | 1.607 | |
| filter_by_cv | 0.181 | 0.020 | 0.200 | |
| gen_lipidsets | 0.221 | 0.032 | 0.252 | |
| lipidDefaults | 0.016 | 0.004 | 0.020 | |
| lipidnames_pattern | 0.000 | 0.002 | 0.002 | |
| lipidr-data | 0.108 | 0.017 | 0.125 | |
| lsea | 2.504 | 0.392 | 2.911 | |
| mva | 3.590 | 0.116 | 3.707 | |
| mw | 0 | 0 | 0 | |
| non_parsed_molecules | 0.108 | 0.020 | 0.129 | |
| normalize_istd | 1.412 | 0.000 | 1.412 | |
| normalize_pqn | 1.246 | 0.008 | 1.253 | |
| pipe | 0.126 | 0.044 | 0.171 | |
| plot_chain_distribution | 1.278 | 0.008 | 1.286 | |
| plot_heatmap | 5.204 | 0.032 | 5.479 | |
| plot_lipidclass | 2.975 | 0.036 | 3.012 | |
| plot_molecules | 4.666 | 0.032 | 4.698 | |
| plot_samples | 2.543 | 0.027 | 2.575 | |
| plot_trend | 0.650 | 0.016 | 0.666 | |
| read_skyline | 0.689 | 0.012 | 0.701 | |
| remove_non_parsed_molecules | 0.111 | 0.036 | 0.147 | |
| set_attr | 0.12 | 0.02 | 0.14 | |
| summarize_transitions | 0.78 | 0.00 | 0.78 | |
| update_molecule_names | 0.184 | 0.024 | 0.208 | |
| use_interactive_graphics | 0.118 | 0.032 | 0.150 | |