Back to Build/check report for BioC 3.21 experimental data |
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This page was generated on 2025-08-21 15:01 -0400 (Thu, 21 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
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 53/432 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
ChAMPdata 2.40.0 (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: 2.40.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChAMPdata_2.40.0.tar.gz |
StartedAt: 2025-08-21 12:02:29 -0400 (Thu, 21 Aug 2025) |
EndedAt: 2025-08-21 12:07:05 -0400 (Thu, 21 Aug 2025) |
EllapsedTime: 276.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChAMPdata.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ChAMPdata_2.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/ChAMPdata.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘ChAMPdata/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChAMPdata’ version ‘2.40.0’ * 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 31.921 0.930 32.856 testDataSet 9.308 0.222 9.534 * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/ChAMPdata.Rcheck/00check.log’ for details.
ChAMPdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ChAMPdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ChAMPdata’ ... ** this is package ‘ChAMPdata’ version ‘2.40.0’ ** 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 | 2.618 | 0.060 | 2.678 | |
AnnoEPIC | 3.778 | 0.084 | 3.862 | |
CellTypeMeans27K | 0.001 | 0.001 | 0.002 | |
CellTypeMeans450K | 0.159 | 0.000 | 0.159 | |
ChAMPdata-package | 31.921 | 0.930 | 32.856 | |
ControlProbes450K | 0.000 | 0.001 | 0.001 | |
ControlProbesEPIC | 0.000 | 0.001 | 0.001 | |
EPIC.manifest.hg19 | 4.410 | 0.193 | 4.604 | |
EPIC.manifest.pop.hg19 | 2.434 | 0.025 | 2.459 | |
EPICSimData | 2.826 | 0.064 | 2.890 | |
MatchGeneName | 0.019 | 0.000 | 0.019 | |
PathwayList | 0.396 | 0.016 | 0.411 | |
bloodCtl | 0.001 | 0.001 | 0.001 | |
hm450.manifest.hg19 | 1.741 | 0.023 | 1.763 | |
hm450.manifest.pop.hg19 | 0.979 | 0.013 | 0.992 | |
hprdAsigH | 2.067 | 0.231 | 2.298 | |
illumina450Gr | 3.461 | 0.066 | 3.527 | |
illuminaEPICGr | 4.074 | 0.012 | 4.088 | |
multi.hit | 0.799 | 0.007 | 0.807 | |
probe.features | 0.656 | 0.007 | 0.664 | |
probe.features.epic | 1.622 | 0.013 | 1.635 | |
probeInfoALL.epic.lv | 0.684 | 0.001 | 0.685 | |
probeInfoALL.lv | 0.472 | 0.002 | 0.474 | |
snp.hit | 0.789 | 0.005 | 0.794 | |
testDataSet | 9.308 | 0.222 | 9.534 | |