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CHECK report for hgu2beta7 on malbec2

This page was generated on 2021-01-14 15:59:03 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE hgu2beta7 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 171/385HostnameOS / ArchINSTALLBUILDCHECK
hgu2beta7 1.31.0
Bioconductor Package Maintainer
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/hgu2beta7
Branch: master
Last Commit: 1142ddf
Last Changed Date: 2020-10-27 09:46:31 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS 

Summary

Package: hgu2beta7
Version: 1.31.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:hgu2beta7.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings hgu2beta7_1.31.0.tar.gz
StartedAt: 2021-01-14 12:15:12 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:15:34 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 22.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: hgu2beta7.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:hgu2beta7.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings hgu2beta7_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/hgu2beta7.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hgu2beta7/DESCRIPTION’ ... OK
* this is package ‘hgu2beta7’ version ‘1.31.0’
* 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 ‘hgu2beta7’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
* 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 ... WARNING
Subdirectory ‘data’ contains no data sets.
* 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
hgu2beta7: no visible binding for global variable ‘hgu2beta7QC’
Undefined global functions or variables:
  hgu2beta7QC
* 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 ... WARNING
'library' or 'require' call not declared from: ‘annotate’
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘Rdata.rdb’ ‘Rdata.rds’ ‘Rdata.rdx’
Please use e.g. ‘inst/extdata’ for non-R data files

* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/hgu2beta7.Rcheck/00check.log’
for details.



Installation output

hgu2beta7.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL hgu2beta7
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘hgu2beta7’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** 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 (hgu2beta7)

Tests output


Example timings

hgu2beta7.Rcheck/hgu2beta7-Ex.timings

nameusersystemelapsed
hgu2beta7ACCNUM0.0870.0040.091
hgu2beta7CHR0.0170.0040.021
hgu2beta7CHRLENGTHS000
hgu2beta7CHRLOC0.130.000.13
hgu2beta7ENZYME0.0170.0000.018
hgu2beta7ENZYME2PROBE0.0020.0000.001
hgu2beta7GENENAME0.0310.0000.031
hgu2beta7GO0.1590.0160.176
hgu2beta7GO2ALLPROBES0.1820.0040.186
hgu2beta7GO2PROBE0.0300.0030.034
hgu2beta7GRIF0.0210.0000.021
hgu2beta7LOCUSID0.0250.0000.025
hgu2beta7MAP0.0750.0000.075
hgu2beta7OMIM0.0220.0000.023
hgu2beta7ORGANISM000
hgu2beta7PATH0.1350.0000.135
hgu2beta7PATH2PROBE0.0030.0000.002
hgu2beta7PMID0.0710.0000.071
hgu2beta7PMID2PROBE0.1960.0120.208
hgu2beta7REFSEQ0.0640.0080.072
hgu2beta7SUMFUNC0.1040.0000.105
hgu2beta7SYMBOL0.0290.0000.030
hgu2beta7UNIGENE0.0320.0000.031