| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:33 -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 TRESS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TRESS.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 2077/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TRESS 1.5.0 (landing page) Zhenxing Guo
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: TRESS |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TRESS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TRESS_1.5.0.tar.gz |
| StartedAt: 2023-02-07 18:10:01 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 18:16:00 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 359.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TRESS.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TRESS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TRESS_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TRESS.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 ‘TRESS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TRESS’ version ‘1.5.0’
* 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 ‘TRESS’ 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 ... NOTE
checkRd: (-1) CallCandidates.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) CallCandidates.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.multiRep.Rd:7: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.paramEsti.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) CallPeaks.paramEsti.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) findBumps.Rd:8: Escaped LaTeX specials: \&
* 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 ... ERROR
Running examples in ‘TRESS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CallDMRs.paramEsti
> ### Title: Model fitting and parameter estimation by TRESS for each
> ### candidate DMR.
> ### Aliases: CallDMRs.paramEsti
>
> ### ** Examples
>
> # A toy example
> data(DMR_M3vsWT) # data from TRESS
> variable = data.frame(predictor = rep(c("WT", "M3"), c(2, 2)))
> model = ~1+predictor
> DMRfit = CallDMRs.paramEsti(
+ counts = DMR_M3vsWT$Counts,
+ sf = DMR_M3vsWT$sf,
+ variable = variable,
+ model = model
+ )
[1] "Start to estimate preliminary MLE ..."
Iteration: 1 log.lik: -41.87843
Iteration: 2 log.lik: -41.86087
Iteration: 3 log.lik: -41.86087
Iteration: 1 log.lik: -47.18917
Iteration: 1 log.lik: -42.3622
Iteration: 2 log.lik: -42.36201
Iteration: 2 log.lik: -47.17211
Iteration: 3 log.lik: -47.17211
Iteration: 1 log.lik: -47.48631
Iteration: 2 log.lik: -47.48607
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Iteration: 1 log.lik: -35.91151
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Iteration: 2 log.lik: -35.90015
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Iteration: 3 log.lik: -35.90015
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Iteration: 1 log.lik: -38.61506
194
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Iteration: 2 log.lik: -38.61442
195
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Iteration: 1 log.lik: -32.68117
Iteration: 2 log.lik: -32.66382
Iteration: 3 log.lik: -32.66382
Iteration: 1 log.lik: -36.62714
Iteration: 2 log.lik: -36.62682
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Iteration: 1 log.lik: -35.21016
Iteration: 2 log.lik: -34.99725
Iteration: 3 log.lik: -34.99716
Iteration: 1 log.lik: -36.11504
Iteration: 2 log.lik: -36.08369
Iteration: 3 log.lik: -36.08369
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Iteration: 1 log.lik: -41.95412
Iteration: 2 log.lik: -41.94335
Iteration: 3 log.lik: -41.94335
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Iteration: 2 log.lik: -43.01255
Iteration: 3 log.lik: -43.01247
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Warning in mclapply(seq_len(nrow(Ratio)), iMLE, X, Y, sx, sy, Ratio, D, :
scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected
Error in matrix(unlist(res.MLE), nrow = length(res.MLE), byrow = TRUE) :
'data' must be of a vector type, was 'NULL'
Calls: CallDMRs.paramEsti -> MLE.parallel -> matrix
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘TRESS.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘TRESS.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/TRESS.Rcheck/vign_test/TRESS/vignettes/TRESS_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/TRESS.Rcheck/vign_test/TRESS/vignettes/TRESS_files/figure-html/unnamed-chunk-20-1.png" but not available.
Quitting from lines 746-757 (TRESS.Rmd)
Error: processing vignette 'TRESS.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': subscript out of bounds
--- failed re-building ‘TRESS.Rmd’
SUMMARY: processing the following file failed:
‘TRESS.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/TRESS.Rcheck/00check.log’
for details.
TRESS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TRESS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘TRESS’ ... ** 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 (TRESS)
TRESS.Rcheck/TRESS-Ex.timings
| name | user | system | elapsed | |
| CallCandidates | 2.123 | 0.087 | 2.467 | |