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BioC experimental data: CHECK report for hgu2beta7 on zin1

This page was generated on 2016-09-17 20:14:52 -0700 (Sat, 17 Sep 2016).

Package 142/304HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hgu2beta7 1.13.0
Bioconductor Package Maintainer
Snapshot Date: 2016-09-17 09:20:18 -0700 (Sat, 17 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/hgu2beta7
Last Changed Rev: 3763 / Revision: 3889
Last Changed Date: 2016-05-03 14:48:02 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: hgu2beta7
Version: 1.13.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings hgu2beta7_1.13.0.tar.gz
StartedAt: 2016-09-17 11:48:52 -0700 (Sat, 17 Sep 2016)
EndedAt: 2016-09-17 11:49:19 -0700 (Sat, 17 Sep 2016)
EllapsedTime: 27.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: hgu2beta7.Rcheck
Warnings: 3

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings hgu2beta7_1.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/hgu2beta7.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.13.0’
* 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 ‘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 loading without being on the library search path ... 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-data-experiment/meat/hgu2beta7.Rcheck/00check.log’
for details.


hgu2beta7.Rcheck/00install.out:

* installing *source* package ‘hgu2beta7’ ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (hgu2beta7)

hgu2beta7.Rcheck/hgu2beta7-Ex.timings:

nameusersystemelapsed
hgu2beta7ACCNUM0.1480.2120.359
hgu2beta7CHR0.0680.0040.074
hgu2beta7CHRLENGTHS0.0040.0000.000
hgu2beta7CHRLOC0.0360.0000.037
hgu2beta7ENZYME0.0480.0000.046
hgu2beta7ENZYME2PROBE0.0040.0000.003
hgu2beta7GENENAME0.1080.0040.109
hgu2beta7GO0.4760.5801.055
hgu2beta7GO2ALLPROBES0.1960.4160.611
hgu2beta7GO2PROBE0.0360.0000.037
hgu2beta7GRIF0.0440.0000.042
hgu2beta7LOCUSID0.0240.0000.024
hgu2beta7MAP0.0280.0000.028
hgu2beta7OMIM0.0240.0040.029
hgu2beta7ORGANISM0.0000.0000.001
hgu2beta7PATH0.1440.0000.143
hgu2beta7PATH2PROBE0.0000.0000.004
hgu2beta7PMID0.0840.0000.087
hgu2beta7PMID2PROBE0.5440.0040.548
hgu2beta7REFSEQ0.1040.0000.107
hgu2beta7SUMFUNC0.1320.1680.301
hgu2beta7SYMBOL0.1440.0000.142
hgu2beta7UNIGENE0.0880.0000.086