| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:05 -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 ChAMP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChAMP.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 312/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChAMP 2.31.0 (landing page) Yuan Tian
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: ChAMP |
| Version: 2.31.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChAMP_2.31.0.tar.gz |
| StartedAt: 2023-05-26 04:35:45 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:35:55 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 10.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ChAMP.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChAMP.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChAMP_2.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChAMP.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ChAMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMP’ version ‘2.31.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
NOTE
Depends: includes the non-default packages:
'minfi', 'ChAMPdata', 'DMRcate', 'Illumina450ProbeVariants.db',
'IlluminaHumanMethylationEPICmanifest', 'DT', 'RPMM'
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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChAMP’ can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores)
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP'
Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP'
Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP'
Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP'
Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP'
Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP'
See ‘/home/biocbuild/bbs-3.18-bioc/meat/ChAMP.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... 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:
‘rmarkdown’
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 ... NOTE
Problems with news in ‘inst/NEWS.Rd’:
NEWS.Rd: Sections \title, and \name must exist and be unique in Rd files
* 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 loading without being on the library search path ... 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘ChAMP.Rmd’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘ChAMP.Rmd’
...
> proc.time()
user system elapsed
0.167 0.029 0.192
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) :
Error writing to connection: No space left on device
* DONE
Status: 2 ERRORs, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/ChAMP.Rcheck/00check.log’
for details.
ChAMP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ChAMP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘ChAMP’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' Note: possible error in 'dmrcate(myannotation, ': unused argument (mc.cores = cores) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' ** testing if installed package can be loaded from final location No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP' Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' Warning: replacing previous import 'plotly::subplot' by 'Hmisc::subplot' when loading 'ChAMP' Warning: replacing previous import 'plyr::summarize' by 'Hmisc::summarize' when loading 'ChAMP' Warning: replacing previous import 'plyr::is.discrete' by 'Hmisc::is.discrete' when loading 'ChAMP' Warning: replacing previous import 'GenomicRanges::sort' by 'globaltest::sort' when loading 'ChAMP' Warning: replacing previous import 'plotly::last_plot' by 'ggplot2::last_plot' when loading 'ChAMP' Warning: replacing previous import 'globaltest::model.matrix' by 'stats::model.matrix' when loading 'ChAMP' Warning: replacing previous import 'globaltest::p.adjust' by 'stats::p.adjust' when loading 'ChAMP' ** testing if installed package keeps a record of temporary installation path * DONE (ChAMP)