Yuan Tian
| Snapshot Date: 2024-03-26 07:30:03 -0400 (Tue, 26 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/ChAMPdata |
| git_branch: devel |
| git_last_commit: 3f2a125 |
| git_last_commit_date: 2023-10-24 09:06:53 -0400 (Tue, 24 Oct 2023) |
| Back to Build/check report for BioC 3.19 experimental data |
|
This page was generated on 2024-03-26 14:51:26 -0400 (Tue, 26 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
| 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 52/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| ChAMPdata 2.35.0 (landing page) Yuan Tian
| nebbiolo1 | Linux (Ubuntu 22.04.3 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: 2.35.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChAMPdata_2.35.0.tar.gz |
| StartedAt: 2024-03-26 11:20:22 -0400 (Tue, 26 Mar 2024) |
| EndedAt: 2024-03-26 11:24:58 -0400 (Tue, 26 Mar 2024) |
| EllapsedTime: 275.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChAMPdata.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChAMPdata_2.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/ChAMPdata.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.35.0’
* 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 730.2Mb
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
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 32.248 1.040 33.298
testDataSet 9.340 0.224 9.570
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.19-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.
ChAMPdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ChAMPdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 | 2.578 | 0.047 | 2.627 | |
| AnnoEPIC | 3.698 | 0.067 | 3.767 | |
| CellTypeMeans27K | 0.002 | 0.000 | 0.002 | |
| CellTypeMeans450K | 0.001 | 0.001 | 0.002 | |
| ChAMPdata-package | 32.248 | 1.040 | 33.298 | |
| ControlProbes450K | 0.000 | 0.000 | 0.001 | |
| ControlProbesEPIC | 0.001 | 0.000 | 0.001 | |
| EPIC.manifest.hg19 | 4.427 | 0.220 | 4.647 | |
| EPIC.manifest.pop.hg19 | 2.557 | 0.068 | 2.625 | |
| EPICSimData | 2.453 | 0.108 | 2.561 | |
| MatchGeneName | 0.019 | 0.000 | 0.021 | |
| PathwayList | 0.391 | 0.012 | 0.404 | |
| bloodCtl | 0.001 | 0.000 | 0.002 | |
| hm450.manifest.hg19 | 1.771 | 0.032 | 1.804 | |
| hm450.manifest.pop.hg19 | 1.976 | 0.064 | 2.041 | |
| hprdAsigH | 2.140 | 0.276 | 2.415 | |
| illumina450Gr | 2.983 | 0.036 | 3.019 | |
| illuminaEPICGr | 3.950 | 0.052 | 4.002 | |
| multi.hit | 1.048 | 0.068 | 1.121 | |
| probe.features | 0.64 | 0.00 | 0.64 | |
| probe.features.epic | 1.489 | 0.012 | 1.501 | |
| probeInfoALL.epic.lv | 0.627 | 0.008 | 0.635 | |
| probeInfoALL.lv | 0.455 | 0.004 | 0.459 | |
| snp.hit | 0.782 | 0.008 | 0.791 | |
| testDataSet | 9.340 | 0.224 | 9.570 | |