| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-29 16:34:11 -0000 (Sun, 29 Jan 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" | 4021 |
| 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 | ||||
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To the developers/maintainers of the RnBeads package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnBeads.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 1696/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RnBeads 2.17.0 (landing page) Fabian Mueller
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: RnBeads |
| Version: 2.17.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz |
| StartedAt: 2023-01-29 07:52:47 -0000 (Sun, 29 Jan 2023) |
| EndedAt: 2023-01-29 08:03:47 -0000 (Sun, 29 Jan 2023) |
| EllapsedTime: 660.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RnBeads.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RnBeads.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 ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘2.17.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
'ff', 'fields', 'ggplot2', 'gplots', 'grid', 'gridExtra', 'limma',
'matrixStats', 'illuminaio', 'methylumi', 'plyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads’ can be installed ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘qvalue’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'RnBeads' was found
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... WARNING
Error in library(RnBeads, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘RnBeads’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'grid'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
'grDevices:::.smoothScatterCalcDensity'
'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
'minfi:::.normalizeFunnorm450k'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Killed
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Killed
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
2023-01-29 08:00:24 1.4 STATUS STARTED Computing Differential Methylation Table
2023-01-29 08:00:24 1.4 INFO Conducting differential analysis using limma
2023-01-29 08:00:24 1.4 STATUS COMPLETED Computing Differential Methylation Table
2023-01-29 08:00:24 1.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-01-29 08:00:26 1.4 STATUS Computed table for tiling
2023-01-29 08:00:26 1.4 STATUS Computed table for genes
2023-01-29 08:00:27 1.4 STATUS Computed table for promoters
2023-01-29 08:00:27 1.4 STATUS Computed table for cpgislands
2023-01-29 08:00:27 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-01-29 08:00:27 1.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-01-29 08:00:27 1.4 STATUS COMPLETED Computing differential methylation tables
2023-01-29 08:00:27 1.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2023-01-29 08:00:27 1.4 STATUS STARTED Testing function: diffVar
2023-01-29 08:00:27 1.4 STATUS STARTED diffVar method
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘RnBeads.Rnw’... failed to complete the test
‘RnBeads_Annotations.Rnw’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘RnBeads.Rnw’
...
> f()
2023-01-29 08:01:24 1.6 STATUS STARTED Another tedious task
2023-01-29 08:01:26 1.6 STATUS STARTED Some tedious subtask
2023-01-29 08:01:28 1.6 STATUS COMPLETED Some tedious subtask
2023-01-29 08:01:28 1.6 STATUS STARTED Another, more tedious subtask
2023-01-29 08:01:31 1.6 STATUS STARTED Some tedious subsubtask
Killed
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 3 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/RnBeads.Rcheck/00check.log’
for details.
RnBeads.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RnBeads ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘RnBeads’ ... ** 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 (RnBeads)
RnBeads.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.
> BiocGenerics:::testPackage("RnBeads")
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpiIJPiN/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package: 'ff'
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following object is masked from 'package:stats4':
mle
The following objects are masked from 'package:base':
backsolve, forwardsolve
Try help(fields) to get started.
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Attaching package: 'grid'
The following object is masked from 'package:ff':
pattern
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
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 objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'scales'
The following object is masked from 'package:viridis':
viridis_pal
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Attaching package: 'MatrixGenerics'
The following object is masked from 'package:Biobase':
rowMedians
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
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following objects are masked from 'package:ff':
mismatch, pattern
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.7 2023-01-02
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:matrixStats':
count
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
2023-01-29 08:00:18 1.1 STATUS STARTED Unit testing: differential
2023-01-29 08:00:18 1.1 STATUS STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2023-01-29 08:00:18 1.1 STATUS COMPLETED Testing function: rowWelchP
2023-01-29 08:00:18 1.1 STATUS STARTED Testing function: limmaP
2023-01-29 08:00:18 1.1 STATUS COMPLETED Testing function: limmaP
2023-01-29 08:00:18 1.1 STATUS STARTED Testing function: computeDiffTab.extended.site
2023-01-29 08:00:18 1.1 INFO Conducting differential analysis using limma
2023-01-29 08:00:18 1.1 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2023-01-29 08:00:18 1.1 STATUS STARTED Testing function: computeDiffTab.default.region
2023-01-29 08:00:18 1.1 INFO Conducting differential analysis using limma
2023-01-29 08:00:22 1.2 STATUS COMPLETED Testing function: computeDiffTab.default.region
2023-01-29 08:00:22 1.2 STATUS STARTED Testing function: combineTestPvalsMeth
2023-01-29 08:00:22 1.2 STATUS COMPLETED Testing function: combineTestPvalsMeth
2023-01-29 08:00:22 1.2 STATUS STARTED Testing function: get.adjustment.variables
2023-01-29 08:00:22 1.2 STATUS COMPLETED Testing function: get.adjustment.variables
2023-01-29 08:00:22 1.2 STATUS STARTED Testing function: get.comparison.info
2023-01-29 08:00:22 1.2 STATUS COMPLETED Testing function: get.comparison.info
2023-01-29 08:00:22 1.2 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2023-01-29 08:00:22 1.2 STATUS STARTED Retrieving comparison info
2023-01-29 08:00:22 1.2 STATUS COMPLETED Retrieving comparison info
2023-01-29 08:00:22 1.2 STATUS STARTED Computing differential methylation tables
2023-01-29 08:00:22 1.2 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-01-29 08:00:22 1.2 STATUS STARTED Computing Differential Methylation Table
2023-01-29 08:00:22 1.2 INFO Conducting differential analysis using limma
2023-01-29 08:00:22 1.2 STATUS COMPLETED Computing Differential Methylation Table
2023-01-29 08:00:22 1.2 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-01-29 08:00:23 1.3 STATUS Computed table for tiling
2023-01-29 08:00:24 1.4 STATUS Computed table for genes
2023-01-29 08:00:24 1.4 STATUS Computed table for promoters
2023-01-29 08:00:24 1.4 STATUS Computed table for cpgislands
2023-01-29 08:00:24 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-01-29 08:00:24 1.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-01-29 08:00:24 1.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-01-29 08:00:24 1.4 STATUS STARTED Computing Differential Methylation Table
2023-01-29 08:00:24 1.4 INFO Conducting differential analysis using limma
2023-01-29 08:00:24 1.4 STATUS COMPLETED Computing Differential Methylation Table
2023-01-29 08:00:24 1.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-01-29 08:00:26 1.4 STATUS Computed table for tiling
2023-01-29 08:00:26 1.4 STATUS Computed table for genes
2023-01-29 08:00:27 1.4 STATUS Computed table for promoters
2023-01-29 08:00:27 1.4 STATUS Computed table for cpgislands
2023-01-29 08:00:27 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-01-29 08:00:27 1.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-01-29 08:00:27 1.4 STATUS COMPLETED Computing differential methylation tables
2023-01-29 08:00:27 1.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2023-01-29 08:00:27 1.4 STATUS STARTED Testing function: diffVar
2023-01-29 08:00:27 1.4 STATUS STARTED diffVar method
Killed