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This page was generated on 2024-04-16 14:51:28 -0400 (Tue, 16 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
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 53/429HostnameOS / ArchINSTALLBUILDCHECK
ChAMPdata 2.34.0  (landing page)
Yuan Tian
Snapshot Date: 2024-04-16 07:30:02 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/ChAMPdata
git_branch: RELEASE_3_18
git_last_commit: debac65
git_last_commit_date: 2023-10-24 09:06:53 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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: 2.34.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ChAMPdata_2.34.0.tar.gz
StartedAt: 2024-04-16 11:09:33 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 11:14:27 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 294.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChAMPdata.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ChAMPdata_2.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘2.34.0’
* 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 730.0Mb
  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  34.857  0.760  36.022
testDataSet        10.055  0.416  10.722
EPIC.manifest.hg19  4.919  0.208   5.206
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.



Installation output

ChAMPdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ChAMPdata
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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
Anno450K2.4310.0402.471
AnnoEPIC3.8230.0713.895
CellTypeMeans27K0.0010.0000.001
CellTypeMeans450K0.0010.0000.001
ChAMPdata-package34.857 0.76036.022
ControlProbes450K0.0010.0000.001
ControlProbesEPIC0.0010.0000.001
EPIC.manifest.hg194.9190.2085.206
EPIC.manifest.pop.hg192.8010.0442.885
EPICSimData3.2260.0443.279
MatchGeneName0.0200.0000.021
PathwayList0.4010.0000.402
bloodCtl0.0010.0000.002
hm450.manifest.hg191.8190.0121.833
hm450.manifest.pop.hg191.1360.0361.175
hprdAsigH2.4130.2602.674
illumina450Gr3.7270.1283.867
illuminaEPICGr4.1790.0004.215
multi.hit0.8430.0000.843
probe.features0.6960.0080.704
probe.features.epic1.7140.0161.732
probeInfoALL.epic.lv0.7710.0040.775
probeInfoALL.lv0.5340.0080.542
snp.hit0.8720.0680.939
testDataSet10.055 0.41610.722