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This page was generated on 2023-05-26 06:18:12 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 mosaics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mosaics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1259/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mosaics 2.39.0 (landing page) Dongjun Chung
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: mosaics |
| Version: 2.39.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data mosaics |
| StartedAt: 2023-05-25 23:54:19 -0000 (Thu, 25 May 2023) |
| EndedAt: 2023-05-25 23:58:11 -0000 (Thu, 25 May 2023) |
| EllapsedTime: 231.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data mosaics
###
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* checking for file ‘mosaics/DESCRIPTION’ ... OK
* preparing ‘mosaics’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘mosaics-example.Rnw’ using Sweave
Loading required package: Rcpp
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Info: reading and preprocessing bin-level data...
Info: data contains only one chromosome.
Info: done!
Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Warning in rlm.default(x, y, weights, method = method, wt.method = wt.method, :
'rlm' failed to converge in 20 steps
Info: done!
Info: fitting one-signal-component model...
Info: fitting two-signal-component model...
Info: calculating BIC of fitted models...
Info: done!
Info: use two-signal-component model.
Info: calculating posterior probabilities...
Info: calling peaks...
Info: done!
Use the provided BAM index file.
Info: done!
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Use the provided BAM index file.
Chromosome information is extracted from the BAM file.
Info: reading the aligned read file and processing it into bin-level files...
Info: done!
Info: reading and preprocessing bin-level data...
Info: data contains only one chromosome.
Info: done!
Info: background estimation based on robust method of moment.
Info: two-sample analysis (Input only).
Info: use adaptive griding.
Info: fitting background model...
Warning in rlm.default(x, y, weights, method = method, wt.method = wt.method, :
'rlm' failed to converge in 20 steps
Info: done!
Info: fitting one-signal-component model...
Info: fitting two-signal-component model...
Info: calculating BIC of fitted models...
Info: done!
Info: initialize MOSAiCS-HMM using MOSAiCS peak calling results.
Info: use two-signal-component model.
Info: initializing HMM parameters...
Info: estimating HMM parameters...
Info: calculating BIC of fitted models...
Info: done!
Info: summarizing ChIP-seq data...
Info: simulating background tags...
Info: simulating ChIP tags for MOSAiCS...
Info: simulating ChIP tags for MOSAiCS-HMM...
Info: peak calling using posterior decoding.
Info: calculating posterior probabilities...
Info: calling peaks...
Info: done!
Info: Loading and processing ChIP sample file...
Info: Single-end tag (SET) is assumed (PET=FALSE).
Info: Average fragment length is set as 200 (fragLen=200).
Info: Use the provided BAM index file.
Info: Reading and processing aligned read file...
Info: Processing and combining peak list and reads...
Info: Calculating coverage...
Info: Done!
Info: Loading and processing matched control sample file...
Info: Single-end tag (SET) is assumed (PET=FALSE).
Info: Average fragment length is set as 200 (fragLen=200).
Info: Use the provided BAM index file.
Info: Reading and processing aligned read file...
Info: Processing and combining peak list and reads...
Info: Calculating coverage...
Info: Done!
Info: reading and preprocessing bin-level data...
Info: assume that data contains only one chromosome
Info: done!
Error: processing vignette 'mosaics-example.Rnw' failed with diagnostics:
unable to run pdflatex on 'mosaics-example.tex'
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.15 ^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘mosaics-example.Rnw’
SUMMARY: processing the following file failed:
‘mosaics-example.Rnw’
Error: Vignette re-building failed.
Execution halted