| Back to Build/check report for BioC 3.23 experimental data |
|
This page was generated on 2026-03-19 15:01 -0400 (Thu, 19 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4858 |
| 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 | ||||
| Package 53/433 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| ChAMPdata 2.43.0 (landing page) Yuan Tian
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||
|
To the developers/maintainers of the ChAMPdata package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ChAMPdata |
| Version: 2.43.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ChAMPdata_2.43.0.tar.gz |
| StartedAt: 2026-03-19 12:05:31 -0400 (Thu, 19 Mar 2026) |
| EndedAt: 2026-03-19 12:10:13 -0400 (Thu, 19 Mar 2026) |
| EllapsedTime: 281.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChAMPdata.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ChAMPdata_2.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-data-experiment/meat/ChAMPdata.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-19 16:05:44 UTC
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.43.0’
* 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 ‘ChAMPdata’ can be installed ... OK
* checking installed package size ... INFO
installed size is 730.2Mb
sub-directories of 1Mb or more:
data 606.3Mb
extdata 123.7Mb
* checking package 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 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
Failed with error: 'there is no package called 'minfi''
Error loading dataset 'bloodCtl':
Error in .requirePackage(package) :
unable to load required package 'minfi'
Failed with error: 'there is no package called 'minfi''
Error loading dataset 'myLoad':
Error in .requirePackage(package) :
unable to load required package 'minfi'
The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChAMPdata-package 31.903 0.886 32.795
testDataSet 9.222 0.237 9.460
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.23-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.
ChAMPdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ChAMPdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ChAMPdata’ ... ** this is package ‘ChAMPdata’ version ‘2.43.0’ ** using staged installation ** data ** inst ** help *** installing help indices ** building package indices ** 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 (ChAMPdata)
ChAMPdata.Rcheck/ChAMPdata-Ex.timings
| name | user | system | elapsed | |
| Anno450K | 2.596 | 0.053 | 2.651 | |
| AnnoEPIC | 3.717 | 0.079 | 3.797 | |
| CellTypeMeans27K | 0.002 | 0.000 | 0.002 | |
| CellTypeMeans450K | 0.002 | 0.000 | 0.001 | |
| ChAMPdata-package | 31.903 | 0.886 | 32.795 | |
| ControlProbes450K | 0.000 | 0.001 | 0.001 | |
| ControlProbesEPIC | 0.001 | 0.000 | 0.001 | |
| EPIC.manifest.hg19 | 4.349 | 0.240 | 4.588 | |
| EPIC.manifest.pop.hg19 | 2.611 | 0.051 | 2.663 | |
| EPICSimData | 1.897 | 0.098 | 1.995 | |
| MatchGeneName | 0.018 | 0.000 | 0.018 | |
| PathwayList | 0.384 | 0.002 | 0.386 | |
| bloodCtl | 0.002 | 0.000 | 0.001 | |
| hm450.manifest.hg19 | 1.691 | 0.032 | 1.722 | |
| hm450.manifest.pop.hg19 | 0.963 | 0.005 | 0.968 | |
| hprdAsigH | 2.022 | 0.266 | 2.288 | |
| illumina450Gr | 3.353 | 0.071 | 3.424 | |
| illuminaEPICGr | 4.057 | 0.013 | 4.078 | |
| multi.hit | 0.787 | 0.007 | 0.794 | |
| probe.features | 0.635 | 0.007 | 0.642 | |
| probe.features.epic | 1.595 | 0.022 | 1.618 | |
| probeInfoALL.epic.lv | 0.685 | 0.002 | 0.686 | |
| probeInfoALL.lv | 0.484 | 0.001 | 0.484 | |
| snp.hit | 0.770 | 0.003 | 0.773 | |
| testDataSet | 9.222 | 0.237 | 9.460 | |