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This page was generated on 2024-05-16 14:51:31 -0400 (Thu, 16 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
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 52/430HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.36.0  (landing page)
Yuan Tian
Snapshot Date: 2024-05-16 07:30:03 -0400 (Thu, 16 May 2024)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_19
git_last_commit: f3d7acf
git_last_commit_date: 2024-04-30 10:40:30 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

CHECK results for ChAMPdata on nebbiolo1


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: 2.36.0
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: 2024-05-16 11:05:23 -0400 (Thu, 16 May 2024)
EndedAt: 2024-05-16 11:09:57 -0400 (Thu, 16 May 2024)
EllapsedTime: 273.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMPdata.Rcheck
Warnings: 1

Command output

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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 4.4.0 (2024-04-24)
* 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 ‘2.36.0’
* 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 31.781  0.987  32.781
testDataSet        9.138  0.240   9.378
* 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.


Installation output

ChAMPdata.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

ChAMPdata.Rcheck/ChAMPdata-Ex.timings

nameusersystemelapsed
Anno450K2.5610.0412.601
AnnoEPIC3.6750.0563.732
CellTypeMeans27K0.0020.0000.002
CellTypeMeans450K0.0010.0000.002
ChAMPdata-package31.781 0.98732.781
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0010.0010.001
EPIC.manifest.hg194.3350.1964.536
EPIC.manifest.pop.hg192.5020.0682.571
EPICSimData2.4050.1312.537
MatchGeneName0.0190.0010.020
PathwayList0.3820.0080.391
bloodCtl0.0010.0000.002
hm450.manifest.hg191.7240.0441.771
hm450.manifest.pop.hg191.7480.0481.797
hprdAsigH2.1030.2482.351
illumina450Gr2.9580.0362.993
illuminaEPICGr4.0430.0484.091
multi.hit1.0550.0481.104
probe.features0.6330.0000.633
probe.features.epic1.4940.0281.522
probeInfoALL.epic.lv0.5970.0200.616
probeInfoALL.lv0.4540.0000.455
snp.hit0.7630.0120.776
testDataSet9.1380.2409.378