Back to Build/check report for BioC 3.21 experimental data |
|
This page was generated on 2025-02-27 15:01 -0500 (Thu, 27 Feb 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4700 |
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 53/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
ChAMPdata 2.39.0 (landing page) Yuan Tian
| nebbiolo1 | 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: 2.39.0 |
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_2.39.0.tar.gz |
StartedAt: 2025-02-27 11:47:44 -0500 (Thu, 27 Feb 2025) |
EndedAt: 2025-02-27 11:52:15 -0500 (Thu, 27 Feb 2025) |
EllapsedTime: 271.7 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_2.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/ChAMPdata.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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 ‘2.39.0’ * 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 31.373 0.920 32.302 testDataSet 8.901 0.222 9.124 * 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 ‘2.39.0’ ** 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 | 2.589 | 0.069 | 2.659 | |
AnnoEPIC | 3.733 | 0.058 | 3.792 | |
CellTypeMeans27K | 0.001 | 0.000 | 0.002 | |
CellTypeMeans450K | 0.172 | 0.000 | 0.172 | |
ChAMPdata-package | 31.373 | 0.920 | 32.302 | |
ControlProbes450K | 0.001 | 0.000 | 0.001 | |
ControlProbesEPIC | 0.001 | 0.000 | 0.001 | |
EPIC.manifest.hg19 | 4.350 | 0.211 | 4.562 | |
EPIC.manifest.pop.hg19 | 2.375 | 0.027 | 2.403 | |
EPICSimData | 2.767 | 0.054 | 2.821 | |
MatchGeneName | 0.018 | 0.001 | 0.019 | |
PathwayList | 0.390 | 0.006 | 0.396 | |
bloodCtl | 0.000 | 0.001 | 0.002 | |
hm450.manifest.hg19 | 1.703 | 0.013 | 1.718 | |
hm450.manifest.pop.hg19 | 0.965 | 0.012 | 0.979 | |
hprdAsigH | 2.075 | 0.246 | 2.322 | |
illumina450Gr | 3.400 | 0.114 | 3.515 | |
illuminaEPICGr | 3.920 | 0.020 | 3.951 | |
multi.hit | 0.761 | 0.005 | 0.767 | |
probe.features | 0.627 | 0.005 | 0.633 | |
probe.features.epic | 1.514 | 0.023 | 1.537 | |
probeInfoALL.epic.lv | 0.635 | 0.006 | 0.641 | |
probeInfoALL.lv | 0.462 | 0.002 | 0.465 | |
snp.hit | 0.747 | 0.007 | 0.754 | |
testDataSet | 8.901 | 0.222 | 9.124 | |