| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:21 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 ADaCGH2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ADaCGH2.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 14/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ADaCGH2 2.39.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: ADaCGH2 |
| Version: 2.39.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ADaCGH2 |
| StartedAt: 2023-04-11 15:45:42 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 15:46:22 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 39.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ADaCGH2
###
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* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* preparing ‘ADaCGH2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ADaCGH2.Rnw’ using Sweave
Loading required package: parallel
Loading required package: ff
Loading required package: bit
Attaching package: ‘bit’
The following object is masked from ‘package:base’:
xor
Attaching package ff
- getOption("fftempdir")=="/tmp/Rtmpgd5vbU/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
Loading required package: GLAD
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Have fun with GLAD
For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008,
If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,
If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,
For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg
######################################################################################
New options are available in daglad: see help for details.
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Read 500 records
Warning in mclapply(X, FUN, ..., mc.preschedule = TRUE, mc.cores = mc.cores, :
all scheduled cores encountered errors in user code
Error: processing vignette 'ADaCGH2.Rnw' failed with diagnostics:
chunk 7
Error in out[[1]]$smoothed : $ operator is invalid for atomic vectors
--- failed re-building ‘ADaCGH2.Rnw’
SUMMARY: processing the following file failed:
‘ADaCGH2.Rnw’
Error: Vignette re-building failed.
Execution halted