| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:28 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the segmentSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmentSeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1817/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| segmentSeq 2.33.0 (landing page) Thomas J. Hardcastle
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: segmentSeq |
| Version: 2.33.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings segmentSeq_2.33.0.tar.gz |
| StartedAt: 2023-02-07 15:16:06 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 15:28:24 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 738.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: segmentSeq.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings segmentSeq_2.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/segmentSeq.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.33.0’
* 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 ‘segmentSeq’ 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 ... NOTE
heuristicSeg : <anonymous>: no visible binding for global variable
‘sDP’
Undefined global functions or variables:
sDP
* 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
classifySeg 40.767 0.593 48.096
lociLikelihoods 18.379 0.008 22.090
heuristicSeg 17.841 0.010 19.559
plotGenome 9.792 0.044 10.486
getCounts 6.663 1.847 26.322
processAD 5.327 0.083 6.120
segData-class 5.283 0.012 5.735
segmentSeq-package 5.287 0.003 5.691
normaliseNC 5.023 0.055 5.348
readMeths 4.043 0.040 5.057
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘methylationAnalysis.Rnw’... failed to complete the test
‘segmentSeq.Rnw’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘methylationAnalysis.Rnw’
...
> if (nrow(sD) != 249271) stop("sD object is the wrong size (should have 249271 rows). Failure.")
> thresh = 0.2
> hS <- heuristicSeg(sD = sD, aD = mD, prop = thresh,
+ cl = cl, gap = 100, getLikes = FALSE)
Number of candidate loci: 249271
Number of candidate nulls: 163635..Killed
... incomplete output. Crash?
when running code in ‘segmentSeq.Rnw’
...
> if (nrow(sD) != 1452) stop("sD object is the wrong size (should have 1452 rows). Failure.")
> hS <- heuristicSeg(sD = sD, aD = aD, RKPM = 1000,
+ largeness = 1e+08, getLikes = TRUE, cl = cl)
Number of candidate loci: 1452
Evaluating candidate loci...done.
>Chr1
Killed
... incomplete output. Crash?
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘methylationAnalysis.Rnw’ using Sweave
Loading required package: baySeq
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 objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: abind
Loading required package: parallel
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: Rsamtools
Loading required package: GenomicAlignments
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
Reading files.......done!
Finding unique cytosines......done!
Processing samples.......done!
Chromosome: Chr1
Finding start-stop co-ordinates...done!
249271 candidate loci found.
Number of candidate loci: 249271
Number of candidate nulls: 163635......done!
Strand *
Checking overlaps.....done.
Selecting loci...done!
Plotting sample: 1
Plotting sample: 2
Plotting sample: 3
Plotting sample: 4
Plotting sample: 1
Plotting sample: 2
Plotting sample: 3
Plotting sample: 4
Finding priors...Killed
--- re-building ‘segmentSeq.Rnw’ using Sweave
Loading required package: baySeq
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 objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: abind
Loading required package: parallel
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: Rsamtools
Loading required package: GenomicAlignments
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
Reading files........done!
Analysing tags...........done!
Chromosome: >Chr1
Finding start-stop co-ordinates...done!
1452 candidate loci found.
Number of candidate loci: 1452
Evaluating candidate loci...done.
>Chr1
Strand *
Checking overlaps.....done.
Selecting loci...done!
Extending loci.....done!
Finding priors...done.
Getting likelihoods for replicate group AGO4...
Length of priorReps:1014
Length of priorSubset:507
Length of subset:507
Length of postRows:507
...done!
Getting likelihoods for replicate group AGO6...
Length of priorReps:1014
Length of priorSubset:507
Length of subset:507
Length of postRows:507
...done!
Finding candidate priors...done.
Finding priors...done.
Segmentation split into 1 parts.
Establishing likelihoods of loci; Part 1 of 1
Establishing likelihoods of loci...
...for replicate group AGO4......done.
...for replicate group AGO6......done.
Killed
SUMMARY: processing the following files failed:
‘methylationAnalysis.Rnw’ ‘segmentSeq.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.
segmentSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL segmentSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘segmentSeq’ ... ** using staged installation ** R ** data ** 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 (segmentSeq)
segmentSeq.Rcheck/segmentSeq-Ex.timings
| name | user | system | elapsed | |
| alignmentData-class | 4.228 | 0.004 | 4.419 | |
| classifySeg | 40.767 | 0.593 | 48.096 | |
| findChunks | 4.287 | 0.004 | 4.888 | |
| getCounts | 6.663 | 1.847 | 26.322 | |
| getOverlaps | 4.297 | 0.012 | 4.932 | |
| heuristicSeg | 17.841 | 0.010 | 19.559 | |
| lociLikelihoods | 18.379 | 0.008 | 22.090 | |
| normaliseNC | 5.023 | 0.055 | 5.348 | |
| plotGenome | 9.792 | 0.044 | 10.486 | |
| processAD | 5.327 | 0.083 | 6.120 | |
| readMethods | 4.181 | 0.008 | 4.782 | |
| readMeths | 4.043 | 0.040 | 5.057 | |
| segData-class | 5.283 | 0.012 | 5.735 | |
| segmentSeq-package | 5.287 | 0.003 | 5.691 | |
| thresholdFinder | 4.055 | 0.080 | 4.624 | |