| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:49 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 52/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AllelicImbalance 1.38.0 (landing page) Jesper R Gadin
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.38.0 |
| 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_1.38.0.tar.gz |
| StartedAt: 2023-10-15 22:26:16 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 22:44:53 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 1116.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AllelicImbalance.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/AllelicImbalance.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AllelicImbalance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AllelicImbalance’ version ‘1.38.0’
* 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 35.655 2.235 48.386
import-bam 30.148 0.429 39.771
lva 20.801 0.096 28.063
scanForHeterozygotes-old 12.019 0.050 15.847
annotation-wrappers 10.256 0.612 13.774
getAlleleCounts 9.594 0.088 12.225
getAlleleQuality 8.486 0.042 10.796
ASEset-glocationplot 7.489 0.189 9.750
LinkVariantAlmlof-plot 4.749 0.037 6.061
ASEset-scanForHeterozygotes 4.249 0.136 5.545
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.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/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/4.3-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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-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)
> 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, 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: 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
35.070 1.965 46.736
AllelicImbalance.Rcheck/AllelicImbalance-Ex.timings
| name | user | system | elapsed | |
| ASEset-barplot | 1.522 | 0.019 | 2.076 | |
| ASEset-class | 1.006 | 0.084 | 1.388 | |
| ASEset-filters | 0.127 | 0.024 | 0.191 | |
| ASEset-gbarplot | 0.090 | 0.017 | 0.138 | |
| ASEset-glocationplot | 7.489 | 0.189 | 9.750 | |
| ASEset-gviztrack | 1.166 | 0.147 | 1.697 | |
| ASEset-scanForHeterozygotes | 4.249 | 0.136 | 5.545 | |
| ASEset.old | 0 | 0 | 0 | |
| ASEset.sim | 0.000 | 0.001 | 0.001 | |
| ASEsetFromBam | 0.003 | 0.005 | 0.008 | |
| DetectedAI-class | 0.232 | 0.007 | 0.305 | |
| DetectedAI-plot | 3.168 | 0.037 | 4.064 | |
| DetectedAI-summary | 0.278 | 0.026 | 0.387 | |
| GRvariants | 0.002 | 0.004 | 0.006 | |
| GlobalAnalysis-class | 0.002 | 0.005 | 0.007 | |
| LinkVariantAlmlof-class | 0.001 | 0.001 | 0.004 | |
| LinkVariantAlmlof-plot | 4.749 | 0.037 | 6.061 | |
| RegionSummary-class | 0.001 | 0.000 | 0.001 | |
| RiskVariant-class | 0.000 | 0.000 | 0.001 | |
| annotation-wrappers | 10.256 | 0.612 | 13.774 | |
| annotationBarplot | 0.000 | 0.001 | 0.001 | |
| barplot-lattice-support | 0.266 | 0.004 | 0.346 | |
| binom.test | 0.117 | 0.006 | 0.158 | |
| chisq.test | 0.319 | 0.006 | 0.414 | |
| cigar-utilities | 0.026 | 0.001 | 0.036 | |
| countAllelesFromBam | 0.002 | 0.005 | 0.007 | |
| coverageMatrixListFromGAL | 1.718 | 0.010 | 2.195 | |
| decorateWithExons | 0.001 | 0.004 | 0.005 | |
| decorateWithGenes | 0.002 | 0.005 | 0.010 | |
| defaultMapBias | 0.071 | 0.009 | 0.102 | |
| defaultPhase | 0.002 | 0.002 | 0.004 | |
| detectAI | 0.217 | 0.010 | 0.288 | |
| fractionPlotDf | 0.074 | 0.008 | 0.102 | |
| gba | 0.000 | 0.001 | 0.000 | |
| genomatrix | 0.000 | 0.001 | 0.001 | |
| genotype2phase | 0.066 | 0.014 | 0.107 | |
| getAlleleCounts | 9.594 | 0.088 | 12.225 | |
| getAlleleQuality | 8.486 | 0.042 | 10.796 | |
| getAreaFromGeneNames | 1.003 | 0.032 | 1.341 | |
| getDefaultMapBiasExpMean | 0.059 | 0.005 | 0.083 | |
| getSnpIdFromLocation | 35.655 | 2.235 | 48.386 | |
| histplot | 0.000 | 0.001 | 0.001 | |
| implodeList-old | 0.011 | 0.001 | 0.016 | |
| import-bam-2 | 0.019 | 0.001 | 0.023 | |
| import-bam | 30.148 | 0.429 | 39.771 | |
| import-bcf | 1.449 | 0.030 | 2.063 | |
| inferAlleles | 0.025 | 0.005 | 0.040 | |
| inferAltAllele | 0.035 | 0.005 | 0.054 | |
| inferGenotypes | 0.070 | 0.004 | 0.101 | |
| initialize-ASEset | 0.179 | 0.003 | 0.234 | |
| initialize-DetectedAI | 0.215 | 0.006 | 0.330 | |
| initialize-GlobalAnalysis | 0.002 | 0.005 | 0.011 | |
| initialize-RiskVariant | 0.002 | 0.004 | 0.006 | |
| legendBarplot | 0.000 | 0.000 | 0.001 | |
| locationplot | 3.469 | 0.045 | 4.901 | |
| lva | 20.801 | 0.096 | 28.063 | |
| lva.internal | 0.756 | 0.010 | 1.011 | |
| makeMaskedFasta | 1.364 | 0.010 | 1.791 | |
| mapBiasRef | 0.026 | 0.006 | 0.041 | |
| minCountFilt | 0.156 | 0.006 | 0.213 | |
| minFreqFilt | 0.155 | 0.006 | 0.211 | |
| multiAllelicFilt | 0.024 | 0.008 | 0.040 | |
| phase2genotype | 0.049 | 0.009 | 0.072 | |
| phaseArray2phaseMatrix | 0.008 | 0.006 | 0.016 | |
| phaseMatrix2Array | 0.008 | 0.005 | 0.019 | |
| randomRef | 0.042 | 0.005 | 0.063 | |
| reads | 0.000 | 0.001 | 0.001 | |
| refAllele | 0.030 | 0.006 | 0.044 | |
| regionSummary | 1.349 | 0.010 | 1.768 | |
| scanForHeterozygotes-old | 12.019 | 0.050 | 15.847 | |