Ahmed Mohamed
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/lipidr |
| git_branch: RELEASE_3_17 |
| git_last_commit: 14a1260 |
| git_last_commit_date: 2023-06-11 08:09:03 -0400 (Sun, 11 Jun 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1071/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| lipidr 2.14.1 (landing page) Ahmed Mohamed
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the lipidr package: - 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. |
| Package: lipidr |
| Version: 2.14.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lipidr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lipidr_2.14.1.tar.gz |
| StartedAt: 2023-10-18 03:54:23 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 04:01:52 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 449.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: lipidr.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lipidr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lipidr_2.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/lipidr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lipidr/DESCRIPTION’ ... OK
* this is package ‘lipidr’ version ‘2.14.1’
* 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 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 startup messages can be suppressed ... 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_results_volcano: no visible binding for global variable ‘AveExpr’
Undefined global functions or variables:
AveExpr
* 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_molecules 5.686 0.071 8.744
lsea 4.129 0.286 6.393
* 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
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/lipidr.Rcheck/00check.log’
for details.
lipidr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lipidr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
0.213 0.065 0.447
lipidr.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, aperm, 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:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
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")'.
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 6 | SKIP 15 | PASS 373 ]
══ Skipped tests (15) ══════════════════════════════════════════════════════════
• On Bioconductor (12): 'test-mw.R:4:3', 'test-mw.R:13:3', 'test-mw.R:26:3',
'test-workflow.R:65:3', 'test-workflow.R:72:3', 'test-workflow.R:79:3',
'test-workflow.R:87:3', 'test-workflow.R:95:3', 'test-workflow.R:104:3',
'test-workflow.R:113:3', 'test-workflow.R:123:3', 'test-workflow.R:151:3'
• empty test (3): 'test-manip.R:14:1', 'test-manip.R:17:1',
'test-readfiles.R:233:1'
[ FAIL 0 | WARN 6 | SKIP 15 | PASS 373 ]
>
> proc.time()
user system elapsed
51.494 2.435 80.046
lipidr.Rcheck/lipidr-Ex.timings
| name | user | system | elapsed | |
| add_sample_annotation | 0.770 | 0.034 | 1.221 | |
| annotate_lipids | 0.137 | 0.002 | 0.205 | |
| data_normalized | 0.040 | 0.004 | 0.068 | |
| de_analysis | 0.819 | 0.027 | 1.299 | |
| filter_by_cv | 0.068 | 0.005 | 0.114 | |
| gen_lipidsets | 0.165 | 0.012 | 0.285 | |
| impute_na | 0.644 | 0.015 | 1.011 | |
| lipidDefaults | 0.007 | 0.002 | 0.013 | |
| lipidnames_pattern | 0.001 | 0.001 | 0.004 | |
| lipidr-data | 0.040 | 0.003 | 0.065 | |
| lsea | 4.129 | 0.286 | 6.393 | |
| mva | 2.773 | 0.106 | 4.344 | |
| mw | 0 | 0 | 0 | |
| non_parsed_molecules | 0.044 | 0.004 | 0.073 | |
| normalize_istd | 0.929 | 0.031 | 1.473 | |
| normalize_pqn | 0.785 | 0.015 | 1.213 | |
| pipe | 0.069 | 0.005 | 0.113 | |
| plot_chain_distribution | 1.081 | 0.018 | 1.671 | |
| plot_lipidclass | 3.053 | 0.040 | 4.680 | |
| plot_molecules | 5.686 | 0.071 | 8.744 | |
| plot_samples | 2.546 | 0.043 | 3.743 | |
| plot_trend | 0.564 | 0.018 | 0.890 | |
| read_skyline | 0.441 | 0.012 | 0.693 | |
| remove_non_parsed_molecules | 0.054 | 0.004 | 0.078 | |
| set_attr | 0.048 | 0.004 | 0.071 | |
| summarize_transitions | 0.617 | 0.013 | 0.934 | |
| update_molecule_names | 0.260 | 0.005 | 0.403 | |
| use_interactive_graphics | 0.149 | 0.017 | 0.255 | |