Jesper R Gadin
| Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/AllelicImbalance |
| git_branch: devel |
| git_last_commit: 13b7eae |
| git_last_commit_date: 2023-10-24 09:56:05 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:38:50 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 54/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AllelicImbalance 1.41.0 (landing page) Jesper R Gadin
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the AllelicImbalance package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AllelicImbalance.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: AllelicImbalance |
| Version: 1.41.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AllelicImbalance_1.41.0.tar.gz |
| StartedAt: 2024-03-01 23:58:04 -0500 (Fri, 01 Mar 2024) |
| EndedAt: 2024-03-02 00:15:02 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 1018.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AllelicImbalance.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AllelicImbalance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AllelicImbalance_1.41.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/AllelicImbalance.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.41.0’
* 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 ‘AllelicImbalance’ 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
CHANGES IN VERSION 1.12.0
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getSnpIdFromLocation 33.767 2.178 41.510
import-bam 29.998 0.513 34.768
lva 20.833 0.183 22.984
scanForHeterozygotes-old 12.068 0.086 13.212
annotation-wrappers 9.327 1.226 12.908
getAlleleCounts 9.757 0.076 10.970
getAlleleQuality 8.579 0.070 9.790
ASEset-glocationplot 7.728 0.263 9.368
LinkVariantAlmlof-plot 4.708 0.040 5.372
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/AllelicImbalance.Rcheck/00check.log’
for details.
AllelicImbalance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AllelicImbalance ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘AllelicImbalance’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance' Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance' ** 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 (AllelicImbalance)
AllelicImbalance.Rcheck/tests/test-all.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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)
> test_check("AllelicImbalance")
Loading required package: AllelicImbalance
Loading required package: grid
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: 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: 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: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_utils.R:3:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 96 ]
>
>
>
> proc.time()
user system elapsed
35.935 2.126 41.909
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
| name | user | system | elapsed | |
| ASEset-barplot | 0.458 | 0.036 | 0.564 | |
| ASEset-class | 0.992 | 0.022 | 1.183 | |
| ASEset-filters | 0.130 | 0.023 | 0.181 | |
| ASEset-gbarplot | 0.090 | 0.017 | 0.125 | |
| ASEset-glocationplot | 7.728 | 0.263 | 9.368 | |
| ASEset-gviztrack | 1.158 | 0.143 | 1.483 | |
| ASEset-scanForHeterozygotes | 4.319 | 0.052 | 4.942 | |
| ASEset.old | 0.000 | 0.001 | 0.000 | |
| ASEset.sim | 0.000 | 0.000 | 0.001 | |
| ASEsetFromBam | 0.002 | 0.004 | 0.006 | |
| DetectedAI-class | 0.228 | 0.007 | 0.259 | |
| DetectedAI-plot | 3.205 | 0.049 | 3.706 | |
| DetectedAI-summary | 0.280 | 0.025 | 0.340 | |
| GRvariants | 0.002 | 0.005 | 0.008 | |
| GlobalAnalysis-class | 0.002 | 0.004 | 0.006 | |
| LinkVariantAlmlof-class | 0.000 | 0.000 | 0.001 | |
| LinkVariantAlmlof-plot | 4.708 | 0.040 | 5.372 | |
| RegionSummary-class | 0.000 | 0.001 | 0.001 | |
| RiskVariant-class | 0.000 | 0.001 | 0.001 | |
| annotation-wrappers | 9.327 | 1.226 | 12.908 | |
| annotationBarplot | 0.000 | 0.000 | 0.001 | |
| barplot-lattice-support | 0.272 | 0.005 | 0.312 | |
| binom.test | 0.113 | 0.007 | 0.139 | |
| chisq.test | 0.319 | 0.007 | 0.359 | |
| cigar-utilities | 0.022 | 0.002 | 0.025 | |
| countAllelesFromBam | 0.002 | 0.005 | 0.007 | |
| coverageMatrixListFromGAL | 1.737 | 0.011 | 1.958 | |
| decorateWithExons | 0.002 | 0.004 | 0.007 | |
| decorateWithGenes | 0.002 | 0.004 | 0.007 | |
| defaultMapBias | 0.074 | 0.007 | 0.094 | |
| defaultPhase | 0.001 | 0.001 | 0.002 | |
| detectAI | 0.217 | 0.006 | 0.249 | |
| fractionPlotDf | 0.074 | 0.005 | 0.087 | |
| gba | 0.000 | 0.000 | 0.001 | |
| genomatrix | 0.000 | 0.000 | 0.001 | |
| genotype2phase | 0.063 | 0.010 | 0.078 | |
| getAlleleCounts | 9.757 | 0.076 | 10.970 | |
| getAlleleQuality | 8.579 | 0.070 | 9.790 | |
| getAreaFromGeneNames | 1.317 | 0.046 | 1.518 | |
| getDefaultMapBiasExpMean | 0.060 | 0.004 | 0.073 | |
| getSnpIdFromLocation | 33.767 | 2.178 | 41.510 | |
| histplot | 0.001 | 0.000 | 0.002 | |
| implodeList-old | 0.011 | 0.001 | 0.017 | |
| import-bam-2 | 0.021 | 0.001 | 0.030 | |
| import-bam | 29.998 | 0.513 | 34.768 | |
| import-bcf | 1.509 | 0.033 | 1.733 | |
| inferAlleles | 0.024 | 0.005 | 0.033 | |
| inferAltAllele | 0.037 | 0.005 | 0.046 | |
| inferGenotypes | 0.073 | 0.006 | 0.088 | |
| initialize-ASEset | 0.191 | 0.005 | 0.227 | |
| initialize-DetectedAI | 0.220 | 0.006 | 0.259 | |
| initialize-GlobalAnalysis | 0.002 | 0.005 | 0.008 | |
| initialize-RiskVariant | 0.002 | 0.004 | 0.008 | |
| legendBarplot | 0 | 0 | 0 | |
| locationplot | 3.482 | 0.057 | 3.971 | |
| lva | 20.833 | 0.183 | 22.984 | |
| lva.internal | 0.767 | 0.011 | 0.854 | |
| makeMaskedFasta | 1.315 | 0.014 | 1.431 | |
| mapBiasRef | 0.027 | 0.006 | 0.036 | |
| minCountFilt | 0.158 | 0.007 | 0.180 | |
| minFreqFilt | 0.159 | 0.007 | 0.179 | |
| multiAllelicFilt | 0.025 | 0.008 | 0.036 | |
| phase2genotype | 0.050 | 0.009 | 0.065 | |
| phaseArray2phaseMatrix | 0.008 | 0.006 | 0.016 | |
| phaseMatrix2Array | 0.007 | 0.005 | 0.012 | |
| randomRef | 0.040 | 0.005 | 0.050 | |
| reads | 0.000 | 0.000 | 0.001 | |
| refAllele | 0.031 | 0.006 | 0.041 | |
| regionSummary | 1.308 | 0.013 | 1.432 | |
| scanForHeterozygotes-old | 12.068 | 0.086 | 13.212 | |