| Back to Build/check report for BioC 3.13 experimental data |
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This page was generated on 2021-10-16 15:58:39 -0400 (Sat, 16 Oct 2021).
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To the developers/maintainers of the ChAMPdata package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 58/406 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| ChAMPdata 2.24.0 (landing page) Yuan Tian
| malbec2 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | ||||||||
| Package: ChAMPdata |
| Version: 2.24.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChAMPdata_2.24.0.tar.gz |
| StartedAt: 2021-10-16 12:55:47 -0400 (Sat, 16 Oct 2021) |
| EndedAt: 2021-10-16 13:00:38 -0400 (Sat, 16 Oct 2021) |
| EllapsedTime: 290.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChAMPdata.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ChAMPdata.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ChAMPdata_2.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/ChAMPdata.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChAMPdata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChAMPdata’ version ‘2.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 743.0Mb
sub-directories of 1Mb or more:
data 619.3Mb
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 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 ... NOTE
Error loading dataset 'bloodCtl':
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "elementMetadata" for this object of class "RGChannelSetExtended"
Error loading dataset 'myLoad':
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'nrow': no slot of name "elementMetadata" for this object of class "MethylSet"
* 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 31.396 0.535 31.934
testDataSet 9.245 0.104 9.350
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.13-data-experiment/meat/ChAMPdata.Rcheck/00check.log’
for details.
ChAMPdata.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ChAMPdata ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 | 2.739 | 0.044 | 2.784 | |
| AnnoEPIC | 4.115 | 0.032 | 4.147 | |
| CellTypeMeans27K | 0.002 | 0.000 | 0.002 | |
| CellTypeMeans450K | 0.001 | 0.000 | 0.002 | |
| ChAMPdata-package | 31.396 | 0.535 | 31.934 | |
| ControlProbes450K | 0.000 | 0.000 | 0.001 | |
| ControlProbesEPIC | 0.001 | 0.000 | 0.001 | |
| EPIC.manifest.hg19 | 4.617 | 0.132 | 4.749 | |
| EPIC.manifest.pop.hg19 | 2.624 | 0.004 | 2.629 | |
| EPICSimData | 2.977 | 0.032 | 3.009 | |
| MatchGeneName | 0.019 | 0.000 | 0.019 | |
| PathwayList | 0.418 | 0.000 | 0.418 | |
| bloodCtl | 0.001 | 0.000 | 0.001 | |
| hm450.manifest.hg19 | 1.740 | 0.008 | 1.749 | |
| hm450.manifest.pop.hg19 | 1.081 | 0.004 | 1.085 | |
| hprdAsigH | 2.540 | 0.208 | 2.748 | |
| illumina450Gr | 2.205 | 0.044 | 2.249 | |
| illuminaEPICGr | 2.559 | 0.008 | 2.567 | |
| multi.hit | 0.785 | 0.000 | 0.785 | |
| probe.features | 0.651 | 0.004 | 0.655 | |
| probe.features.epic | 1.627 | 0.004 | 1.630 | |
| probeInfoALL.epic.lv | 0.687 | 0.004 | 0.690 | |
| probeInfoALL.lv | 0.492 | 0.004 | 0.495 | |
| snp.hit | 0.818 | 0.000 | 0.818 | |
| testDataSet | 9.245 | 0.104 | 9.350 | |