| Back to Build/check report for BioC 3.17 experimental data |
|
This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| 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 53/421 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| ChAMPdata 2.32.0 (landing page) Yuan Tian
| nebbiolo1 | Linux (Ubuntu 22.04.2 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: 2.32.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChAMPdata_2.32.0.tar.gz |
| StartedAt: 2023-10-12 11:05:04 -0400 (Thu, 12 Oct 2023) |
| EndedAt: 2023-10-12 11:09:39 -0400 (Thu, 12 Oct 2023) |
| EllapsedTime: 275.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChAMPdata.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ChAMPdata_2.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.32.0’
* 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 31.646 1.068 32.725
testDataSet 9.352 0.284 9.636
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.
ChAMPdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ChAMPdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 2.337 | 0.048 | 2.386 | |
| AnnoEPIC | 3.732 | 0.104 | 3.836 | |
| CellTypeMeans27K | 0.002 | 0.000 | 0.002 | |
| CellTypeMeans450K | 0.002 | 0.000 | 0.002 | |
| ChAMPdata-package | 31.646 | 1.068 | 32.725 | |
| ControlProbes450K | 0.000 | 0.000 | 0.001 | |
| ControlProbesEPIC | 0.001 | 0.000 | 0.001 | |
| EPIC.manifest.hg19 | 4.579 | 0.184 | 4.763 | |
| EPIC.manifest.pop.hg19 | 2.538 | 0.048 | 2.588 | |
| EPICSimData | 2.864 | 0.100 | 2.963 | |
| MatchGeneName | 0.019 | 0.000 | 0.020 | |
| PathwayList | 0.385 | 0.000 | 0.386 | |
| bloodCtl | 0.001 | 0.000 | 0.001 | |
| hm450.manifest.hg19 | 1.702 | 0.048 | 1.751 | |
| hm450.manifest.pop.hg19 | 1.072 | 0.029 | 1.101 | |
| hprdAsigH | 2.214 | 0.383 | 2.598 | |
| illumina450Gr | 3.421 | 0.080 | 3.501 | |
| illuminaEPICGr | 3.910 | 0.052 | 3.961 | |
| multi.hit | 0.742 | 0.008 | 0.751 | |
| probe.features | 0.636 | 0.020 | 0.656 | |
| probe.features.epic | 1.539 | 0.024 | 1.563 | |
| probeInfoALL.epic.lv | 0.672 | 0.004 | 0.676 | |
| probeInfoALL.lv | 0.461 | 0.012 | 0.473 | |
| snp.hit | 0.759 | 0.000 | 0.760 | |
| testDataSet | 9.352 | 0.284 | 9.636 | |