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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 |
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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 |
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 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data mosaics ### ############################################################################## ############################################################################## * 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