Marcel Ramos
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/TENxIO |
| git_branch: RELEASE_3_17 |
| git_last_commit: f2ae1a5 |
| git_last_commit_date: 2023-04-25 11:40:51 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:13 -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 2082/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TENxIO 1.2.0 (landing page) Marcel Ramos
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the TENxIO 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: TENxIO |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TENxIO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TENxIO_1.2.0.tar.gz |
| StartedAt: 2023-10-19 06:29:08 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 06:35:00 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 351.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TENxIO.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TENxIO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TENxIO_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TENxIO.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 ‘TENxIO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TENxIO’ version ‘1.2.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TENxIO’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TENxFragments 3.762 1.23 8.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.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
TENxIO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TENxIO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘TENxIO’ ... ** 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 (TENxIO)
TENxIO.Rcheck/tests/tinytest.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("tinytest", quietly = TRUE))
+ tinytest::test_package("TENxIO")
Loading required package: SingleCellExperiment
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_TENxFile-class.R......... 1 tests [0;32mOK[0m
test_TENxFile-class.R......... 1 tests [0;32mOK[0m
test_TENxFile-class.R......... 1 tests [0;32mOK[0m
test_TENxFile-class.R......... 2 tests [0;32mOK[0m
test_TENxFile-class.R......... 2 tests [0;32mOK[0m
test_TENxFile-class.R......... 3 tests [0;32mOK[0m
test_TENxFile-class.R......... 3 tests [0;32mOK[0m
test_TENxFile-class.R......... 3 tests [0;32mOK[0m
test_TENxFile-class.R......... 3 tests [0;32mOK[0m
test_TENxFile-class.R......... 4 tests [0;32mOK[0m
test_TENxFile-class.R......... 5 tests [0;32mOK[0m
test_TENxFile-class.R......... 6 tests [0;32mOK[0m
test_TENxFile-class.R......... 6 tests [0;32mOK[0m
test_TENxFile-class.R......... 6 tests [0;32mOK[0m
test_TENxFile-class.R......... 6 tests [0;32mOK[0m
test_TENxFile-class.R......... 6 tests [0;32mOK[0m
test_TENxFile-class.R......... 7 tests [0;32mOK[0m
test_TENxFile-class.R......... 7 tests [0;32mOK[0m
test_TENxFile-class.R......... 7 tests [0;32mOK[0m
test_TENxFile-class.R......... 8 tests [0;32mOK[0m
test_TENxFile-class.R......... 9 tests [0;32mOK[0m [0;34m5.4s[0m
test_TENxFileList-class.R..... 0 tests
test_TENxFileList-class.R..... 0 tests
test_TENxFileList-class.R..... 1 tests [0;32mOK[0m
test_TENxFileList-class.R..... 2 tests [0;32mOK[0m
test_TENxFileList-class.R..... 3 tests [0;32mOK[0m
test_TENxFileList-class.R..... 3 tests [0;32mOK[0m
test_TENxFileList-class.R..... 4 tests [0;32mOK[0m
test_TENxFileList-class.R..... 5 tests [0;32mOK[0m
test_TENxFileList-class.R..... 6 tests [0;32mOK[0m
test_TENxFileList-class.R..... 7 tests [0;32mOK[0m
test_TENxFileList-class.R..... 8 tests [0;32mOK[0m
test_TENxFileList-class.R..... 9 tests [0;32mOK[0m [0;34m1.9s[0m
test_TENxFragments-class.R.... 0 tests
test_TENxFragments-class.R.... 1 tests [0;32mOK[0m
test_TENxFragments-class.R.... 1 tests [0;32mOK[0m
test_TENxFragments-class.R.... 2 tests [0;32mOK[0m
test_TENxFragments-class.R.... 3 tests [0;32mOK[0m
test_TENxFragments-class.R.... 4 tests [0;32mOK[0m
test_TENxFragments-class.R.... 4 tests [0;32mOK[0m
test_TENxFragments-class.R.... 5 tests [0;32mOK[0m
test_TENxFragments-class.R.... 6 tests [0;32mOK[0m
test_TENxFragments-class.R.... 7 tests [0;32mOK[0m [0;34m3.9s[0m
test_TENxH5-class.R........... 0 tests
test_TENxH5-class.R........... 0 tests
test_TENxH5-class.R........... 1 tests [0;32mOK[0m
test_TENxH5-class.R........... 2 tests [0;32mOK[0m
test_TENxH5-class.R........... 2 tests [0;32mOK[0m
test_TENxH5-class.R........... 3 tests [0;32mOK[0m
test_TENxH5-class.R........... 4 tests [0;32mOK[0m
test_TENxH5-class.R........... 4 tests [0;32mOK[0m
test_TENxH5-class.R........... 4 tests [0;32mOK[0m
test_TENxH5-class.R........... 5 tests [0;32mOK[0m
test_TENxH5-class.R........... 6 tests [0;32mOK[0m
test_TENxH5-class.R........... 7 tests [0;32mOK[0m
test_TENxH5-class.R........... 8 tests [0;32mOK[0m
test_TENxH5-class.R........... 9 tests [0;32mOK[0m [0;34m2.1s[0m
test_TENxMTX-class.R.......... 0 tests
test_TENxMTX-class.R.......... 0 tests
test_TENxMTX-class.R.......... 1 tests [0;32mOK[0m
test_TENxMTX-class.R.......... 2 tests [0;32mOK[0m
test_TENxMTX-class.R.......... 3 tests [0;32mOK[0m
test_TENxMTX-class.R.......... 3 tests [0;32mOK[0m
test_TENxMTX-class.R.......... 4 tests [0;32mOK[0m
test_TENxMTX-class.R.......... 5 tests [0;32mOK[0m
test_TENxMTX-class.R.......... 6 tests [0;32mOK[0m [0;36m49ms[0m
test_TENxPeaks-class.R........ 0 tests
test_TENxPeaks-class.R........ 0 tests
test_TENxPeaks-class.R........ 1 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 2 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 2 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 3 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 4 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 5 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 5 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 6 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 7 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 8 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 9 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 10 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 11 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 12 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 13 tests [0;32mOK[0m
test_TENxPeaks-class.R........ 14 tests [0;32mOK[0m [0;34m0.8s[0m
All ok, 54 results (14.1s)
Warning message:
In TENxFragments(fr, extension = "tsv.gz") :
Using default 'yieldSize' parameter
>
> proc.time()
user system elapsed
14.735 1.264 29.111
TENxIO.Rcheck/TENxIO-Ex.timings
| name | user | system | elapsed | |
| TENxFile | 0.000 | 0.000 | 0.001 | |
| TENxFileList | 1.364 | 0.067 | 2.675 | |
| TENxFragments | 3.762 | 1.230 | 8.696 | |
| TENxH5 | 2.176 | 0.146 | 4.511 | |
| TENxMTX | 0.031 | 0.002 | 0.056 | |
| TENxPeaks | 2.144 | 0.083 | 4.000 | |