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This page was generated on 2024-12-03 15:42 -0500 (Tue, 03 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4739
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 53/431HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.38.0  (landing page)
Yuan Tian
Snapshot Date: 2024-12-03 07:30 -0500 (Tue, 03 Dec 2024)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_20
git_last_commit: 373fee5
git_last_commit_date: 2024-10-29 09:37:50 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published


CHECK results for ChAMPdata on nebbiolo2

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.

raw results


Summary

Package: ChAMPdata
Version: 2.38.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChAMPdata_2.38.0.tar.gz
StartedAt: 2024-12-03 11:58:40 -0500 (Tue, 03 Dec 2024)
EndedAt: 2024-12-03 12:06:39 -0500 (Tue, 03 Dec 2024)
EllapsedTime: 479.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMPdata.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ChAMPdata_2.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.38.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 730.0Mb
  sub-directories of 1Mb or more:
    data     606.3Mb
    extdata  123.6Mb
* 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 31.178  0.688  31.868
testDataSet        8.723  0.139   8.863
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.


Installation output

ChAMPdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ChAMPdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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)

Tests output


Example timings

ChAMPdata.Rcheck/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K2.4430.0492.490
AnnoEPIC3.6660.0513.717
CellTypeMeans27K0.0020.0010.002
CellTypeMeans450K0.0010.0010.001
ChAMPdata-package31.178 0.68831.868
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0000.0010.001
EPIC.manifest.hg194.3170.1484.466
EPIC.manifest.pop.hg192.3470.0182.365
EPICSimData2.6530.0402.693
MatchGeneName0.0170.0000.018
PathwayList0.3680.0000.369
bloodCtl0.0000.0010.001
hm450.manifest.hg191.6600.0061.666
hm450.manifest.pop.hg190.9480.0060.954
hprdAsigH2.0130.2682.281
illumina450Gr3.2270.0473.274
illuminaEPICGr3.8550.0043.859
multi.hit0.7470.0000.747
probe.features0.6210.0000.621
probe.features.epic1.4860.0031.489
probeInfoALL.epic.lv0.6230.0020.625
probeInfoALL.lv0.4550.0010.456
snp.hit0.7460.0000.746
testDataSet8.7230.1398.863