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CHECK report for geuvPack on malbec2

This page was generated on 2018-10-16 14:18:51 -0400 (Tue, 16 Oct 2018).

Package 125/342HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geuvPack 1.12.0
VJ Carey
Snapshot Date: 2018-10-16 07:35:22 -0400 (Tue, 16 Oct 2018)
URL: https://git.bioconductor.org/packages/geuvPack
Branch: RELEASE_3_7
Last Commit: 637cee4
Last Changed Date: 2018-04-30 10:31:29 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: geuvPack
Version: 1.12.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:geuvPack.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings geuvPack_1.12.0.tar.gz
StartedAt: 2018-10-16 10:59:34 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 11:02:40 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 185.6 seconds
RetCode: 0
Status:  OK 
CheckDir: geuvPack.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:geuvPack.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings geuvPack_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/geuvPack.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geuvPack/DESCRIPTION’ ... OK
* this is package ‘geuvPack’ version ‘1.12.0’
* 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 ‘geuvPack’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 93.1Mb
  sub-directories of 1Mb or more:
    data  93.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
gtpath: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
  Failed with error:  'package 'DelayedArray' could not be loaded'
  Error in .requirePackage(package) : 
    unable to find required package 'SummarizedExperiment'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
geuFPKM 8.516  0.108   8.629
gsvs    8.192  0.112   8.309
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/geuvPack.Rcheck/00check.log’
for details.



Installation output

geuvPack.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL geuvPack
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘geuvPack’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (geuvPack)

Tests output


Example timings

geuvPack.Rcheck/geuvPack-Ex.timings

nameusersystemelapsed
geuFPKM8.5160.1088.629
gsvs8.1920.1128.309
gtpath0.0000.0000.001