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CHECK report for MetaGxPancreas on malbec1

This page was generated on 2020-04-14 17:46:29 -0400 (Tue, 14 Apr 2020).

Package 217/384HostnameOS / ArchINSTALLBUILDCHECK
MetaGxPancreas 1.6.0
Michael Zon
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/MetaGxPancreas
Branch: RELEASE_3_10
Last Commit: f3dcf43
Last Changed Date: 2019-11-05 04:31:17 -0400 (Tue, 05 Nov 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: MetaGxPancreas
Version: 1.6.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MetaGxPancreas.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MetaGxPancreas_1.6.0.tar.gz
StartedAt: 2020-04-14 13:50:12 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 14:06:15 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 962.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MetaGxPancreas.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MetaGxPancreas.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MetaGxPancreas_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/MetaGxPancreas.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaGxPancreas/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaGxPancreas’ version ‘1.6.0’
* 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 ‘MetaGxPancreas’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
BADEA                36.444  0.652  40.181
GRUTZMANN            35.420  0.324  42.716
loadPancreasEsets    34.852  0.304  37.989
TCGA                 34.512  0.420  39.500
PEI                  34.008  0.420  42.711
loadPancreasDatasets 33.348  0.420  37.112
KIRBY                33.320  0.436  36.339
HAMIDI               33.060  0.420  36.168
ICGCMICRO            33.100  0.308  36.210
JANKY                32.904  0.384  36.485
UNC                  32.676  0.396  40.650
YANG                 32.612  0.396  36.090
ICGCSEQ              32.656  0.276  36.804
WINTER               32.268  0.444  35.300
PCSI                 31.852  0.408  36.898
BALAGURUNATH         31.596  0.496  34.414
OUH                  31.188  0.416  35.664
BAUER                31.156  0.372  34.048
CHEN                 31.224  0.296  34.049
COLLISON             30.920  0.312  33.981
ZHANG                30.624  0.392  33.865
LUNARDI              30.248  0.360  33.701
HAIDER               29.916  0.316  34.314
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘required.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MetaGxPancreas.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MetaGxPancreas
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘MetaGxPancreas’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (MetaGxPancreas)

Tests output

MetaGxPancreas.Rcheck/tests/required.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #
> 
> proc.time()
   user  system elapsed 
  0.152   0.016   0.167 

Example timings

MetaGxPancreas.Rcheck/MetaGxPancreas-Ex.timings

nameusersystemelapsed
BADEA36.444 0.65240.181
BALAGURUNATH31.596 0.49634.414
BAUER31.156 0.37234.048
CHEN31.224 0.29634.049
COLLISON30.920 0.31233.981
GRUTZMANN35.420 0.32442.716
HAIDER29.916 0.31634.314
HAMIDI33.060 0.42036.168
ICGCMICRO33.100 0.30836.210
ICGCSEQ32.656 0.27636.804
JANKY32.904 0.38436.485
KIRBY33.320 0.43636.339
LUNARDI30.248 0.36033.701
OUH31.188 0.41635.664
PCSI31.852 0.40836.898
PEI34.008 0.42042.711
TCGA34.512 0.42039.500
UNC32.676 0.39640.650
WINTER32.268 0.44435.300
YANG32.612 0.39636.090
ZHANG30.624 0.39233.865
loadPancreasDatasets33.348 0.42037.112
loadPancreasEsets34.852 0.30437.989