Back to Build/check report for BioC 3.20 experimental data |
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This page was generated on 2025-01-02 15:42 -0500 (Thu, 02 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
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: 2025-01-02 11:48:10 -0500 (Thu, 02 Jan 2025) |
EndedAt: 2025-01-02 11:52:38 -0500 (Thu, 02 Jan 2025) |
EllapsedTime: 267.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChAMPdata.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/ChAMPdata.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 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 32.187 0.646 32.836 testDataSet 9.092 0.088 9.181 * 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 | 2.592 | 0.066 | 2.658 | |
AnnoEPIC | 3.745 | 0.056 | 3.799 | |
CellTypeMeans27K | 0.002 | 0.000 | 0.001 | |
CellTypeMeans450K | 0.002 | 0.000 | 0.001 | |
ChAMPdata-package | 32.187 | 0.646 | 32.836 | |
ControlProbes450K | 0.001 | 0.000 | 0.001 | |
ControlProbesEPIC | 0.000 | 0.001 | 0.000 | |
EPIC.manifest.hg19 | 4.455 | 0.168 | 4.623 | |
EPIC.manifest.pop.hg19 | 2.406 | 0.023 | 2.430 | |
EPICSimData | 2.735 | 0.093 | 2.828 | |
MatchGeneName | 0.018 | 0.000 | 0.017 | |
PathwayList | 0.376 | 0.001 | 0.377 | |
bloodCtl | 0.001 | 0.000 | 0.001 | |
hm450.manifest.hg19 | 1.692 | 0.006 | 1.698 | |
hm450.manifest.pop.hg19 | 0.970 | 0.004 | 0.974 | |
hprdAsigH | 2.155 | 0.253 | 2.409 | |
illumina450Gr | 3.734 | 0.065 | 3.805 | |
illuminaEPICGr | 4.211 | 0.003 | 4.224 | |
multi.hit | 0.807 | 0.003 | 0.810 | |
probe.features | 0.637 | 0.002 | 0.638 | |
probe.features.epic | 1.584 | 0.006 | 1.590 | |
probeInfoALL.epic.lv | 0.672 | 0.000 | 0.671 | |
probeInfoALL.lv | 0.466 | 0.001 | 0.467 | |
snp.hit | 0.761 | 0.002 | 0.762 | |
testDataSet | 9.092 | 0.088 | 9.181 | |