Leo Lahti
| Snapshot Date: 2024-03-26 07:30:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/microbiomeDataSets |
| git_branch: devel |
| git_last_commit: 28dd609 |
| git_last_commit_date: 2023-10-24 09:21:46 -0400 (Tue, 24 Oct 2023) |
| Back to Build/check report for BioC 3.19 experimental data |
|
This page was generated on 2024-03-26 14:51:27 -0400 (Tue, 26 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
| 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 236/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| microbiomeDataSets 1.11.0 (landing page) Leo Lahti
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | |||||||
|
To the developers/maintainers of the microbiomeDataSets 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: microbiomeDataSets |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:microbiomeDataSets.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings microbiomeDataSets_1.11.0.tar.gz |
| StartedAt: 2024-03-26 11:54:30 -0400 (Tue, 26 Mar 2024) |
| EndedAt: 2024-03-26 12:00:08 -0400 (Tue, 26 Mar 2024) |
| EllapsedTime: 338.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: microbiomeDataSets.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:microbiomeDataSets.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings microbiomeDataSets_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/microbiomeDataSets.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘microbiomeDataSets/DESCRIPTION’ ... OK
* this is package ‘microbiomeDataSets’ version ‘1.11.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following non-portable file path:
microbiomeDataSets/docs/articles/microbiomeDataSets_files/accessible-code-block-0.0.1/empty-anchor.js
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘microbiomeDataSets’ 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) GrieneisenTSData.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) GrieneisenTSData.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HintikkaXOData.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HintikkaXOData.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HintikkaXOData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HintikkaXOData.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HintikkaXOData.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) HintikkaXOData.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) availableDataSets.Rd:12: Lost braces in \itemize; \value handles \item{}{} directly
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GrieneisenTSData 6.628 0.880 8.413
LahtiMLData 6.875 0.524 8.410
SongQAData 5.227 0.584 6.566
HintikkaXOData 5.251 0.559 6.447
SprockettTHData 5.373 0.407 6.487
SilvermanAGutData 4.765 0.428 5.812
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-data-experiment/meat/microbiomeDataSets.Rcheck/00check.log’
for details.
microbiomeDataSets.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL microbiomeDataSets ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘microbiomeDataSets’ ... ** using staged installation ** R ** 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 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 (microbiomeDataSets)
microbiomeDataSets.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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(microbiomeDataSets)
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, 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
Loading required package: TreeSummarizedExperiment
Loading required package: SingleCellExperiment
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: MultiAssayExperiment
>
> test_check("microbiomeDataSets")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
57.515 5.891 69.886
microbiomeDataSets.Rcheck/microbiomeDataSets-Ex.timings
| name | user | system | elapsed | |
| GrieneisenTSData | 6.628 | 0.880 | 8.413 | |
| HintikkaXOData | 5.251 | 0.559 | 6.447 | |
| LahtiMLData | 6.875 | 0.524 | 8.410 | |
| LahtiWAData | 2.990 | 0.336 | 3.750 | |
| OKeefeDSData | 2.972 | 0.264 | 3.811 | |
| SilvermanAGutData | 4.765 | 0.428 | 5.812 | |
| SongQAData | 5.227 | 0.584 | 6.566 | |
| SprockettTHData | 5.373 | 0.407 | 6.487 | |
| availableDataSets | 0.002 | 0.000 | 0.003 | |