| Back to Build/check report for BioC 3.19 experimental data | 
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This page was generated on 2024-10-17 14:51 -0400 (Thu, 17 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 | 
| 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 52/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| ChAMPdata 2.36.0  (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: 2.36.0 | 
| 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_2.36.0.tar.gz | 
| StartedAt: 2024-10-17 11:06:52 -0400 (Thu, 17 Oct 2024) | 
| EndedAt: 2024-10-17 11:11:23 -0400 (Thu, 17 Oct 2024) | 
| EllapsedTime: 270.8 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_2.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.36.0’
* 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 31.583  1.101  32.694
testDataSet        9.312  0.232   9.544
* 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 | 2.551 | 0.056 | 2.608 | |
| AnnoEPIC | 3.721 | 0.068 | 3.791 | |
| CellTypeMeans27K | 0.002 | 0.000 | 0.002 | |
| CellTypeMeans450K | 0.000 | 0.001 | 0.002 | |
| ChAMPdata-package | 31.583 | 1.101 | 32.694 | |
| ControlProbes450K | 0.001 | 0.000 | 0.001 | |
| ControlProbesEPIC | 0.001 | 0.000 | 0.001 | |
| EPIC.manifest.hg19 | 4.381 | 0.232 | 4.615 | |
| EPIC.manifest.pop.hg19 | 2.559 | 0.040 | 2.600 | |
| EPICSimData | 2.756 | 0.100 | 2.856 | |
| MatchGeneName | 0.018 | 0.000 | 0.019 | |
| PathwayList | 0.377 | 0.016 | 0.393 | |
| bloodCtl | 0.001 | 0.000 | 0.001 | |
| hm450.manifest.hg19 | 1.739 | 0.036 | 1.776 | |
| hm450.manifest.pop.hg19 | 1.052 | 0.028 | 1.081 | |
| hprdAsigH | 2.293 | 0.276 | 2.569 | |
| illumina450Gr | 3.420 | 0.084 | 3.505 | |
| illuminaEPICGr | 3.954 | 0.052 | 4.006 | |
| multi.hit | 0.763 | 0.008 | 0.772 | |
| probe.features | 0.658 | 0.008 | 0.667 | |
| probe.features.epic | 1.543 | 0.016 | 1.560 | |
| probeInfoALL.epic.lv | 0.664 | 0.008 | 0.672 | |
| probeInfoALL.lv | 0.452 | 0.000 | 0.453 | |
| snp.hit | 0.746 | 0.016 | 0.764 | |
| testDataSet | 9.312 | 0.232 | 9.544 | |