| Back to Build/check report for BioC 3.20 experimental data |
|
This page was generated on 2025-04-01 15:41 -0400 (Tue, 01 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| 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 53/431 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| ChAMPdata 2.38.0 (landing page) Yuan Tian
| nebbiolo2 | Linux (Ubuntu 24.04.1 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: 2.38.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChAMPdata_2.38.0.tar.gz |
| StartedAt: 2025-04-01 11:47:05 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 11:51:33 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 267.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChAMPdata.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChAMPdata_2.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.38.0’
* 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 ... NOTE
installed size is 730.0Mb
sub-directories of 1Mb or more:
data 606.3Mb
extdata 123.6Mb
* 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
Error loading dataset 'bloodCtl':
Error in .requirePackage(package) :
unable to find required package 'minfi'
Error loading dataset 'myLoad':
Error in .requirePackage(package) :
unable to find 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 32.065 0.714 32.783
testDataSet 9.087 0.125 9.213
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.20-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.
ChAMPdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ChAMPdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ChAMPdata’ ... ** 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 | 2.561 | 0.048 | 2.611 | |
| AnnoEPIC | 3.765 | 0.047 | 3.812 | |
| CellTypeMeans27K | 0.001 | 0.001 | 0.002 | |
| CellTypeMeans450K | 0.001 | 0.001 | 0.002 | |
| ChAMPdata-package | 32.065 | 0.714 | 32.783 | |
| ControlProbes450K | 0.001 | 0.000 | 0.001 | |
| ControlProbesEPIC | 0.001 | 0.000 | 0.001 | |
| EPIC.manifest.hg19 | 4.421 | 0.219 | 4.640 | |
| EPIC.manifest.pop.hg19 | 2.398 | 0.048 | 2.447 | |
| EPICSimData | 2.719 | 0.059 | 2.778 | |
| MatchGeneName | 0.018 | 0.000 | 0.018 | |
| PathwayList | 0.378 | 0.001 | 0.380 | |
| bloodCtl | 0.001 | 0.000 | 0.001 | |
| hm450.manifest.hg19 | 1.690 | 0.013 | 1.703 | |
| hm450.manifest.pop.hg19 | 0.962 | 0.019 | 0.982 | |
| hprdAsigH | 2.023 | 0.264 | 2.288 | |
| illumina450Gr | 3.429 | 0.051 | 3.480 | |
| illuminaEPICGr | 3.995 | 0.003 | 4.004 | |
| multi.hit | 0.771 | 0.002 | 0.773 | |
| probe.features | 0.653 | 0.000 | 0.654 | |
| probe.features.epic | 1.554 | 0.004 | 1.559 | |
| probeInfoALL.epic.lv | 0.661 | 0.002 | 0.663 | |
| probeInfoALL.lv | 0.47 | 0.00 | 0.47 | |
| snp.hit | 0.774 | 0.003 | 0.776 | |
| testDataSet | 9.087 | 0.125 | 9.213 | |