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BioC experimental data: CHECK report for hgu2beta7 on malbec1

This page was generated on 2017-04-15 16:49:26 -0400 (Sat, 15 Apr 2017).

Package 145/310HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hgu2beta7 1.14.0
Bioconductor Package Maintainer
Snapshot Date: 2017-04-15 09:20:05 -0400 (Sat, 15 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_4/experiment/pkgs/hgu2beta7
Last Changed Rev: 3958 / Revision: 4141
Last Changed Date: 2016-10-17 14:47:53 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: hgu2beta7
Version: 1.14.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings hgu2beta7_1.14.0.tar.gz
StartedAt: 2017-04-15 11:00:07 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 11:00:30 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 23.4 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_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/hgu2beta7.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.0’
* 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
hgu2beta7ACCNUM0.1800.0200.199
hgu2beta7CHR0.0720.0000.071
hgu2beta7CHRLENGTHS000
hgu2beta7CHRLOC0.0400.0000.041
hgu2beta7ENZYME0.0240.0080.031
hgu2beta7ENZYME2PROBE0.0040.0000.003
hgu2beta7GENENAME0.1120.0000.115
hgu2beta7GO0.4600.0480.509
hgu2beta7GO2ALLPROBES0.1920.0360.228
hgu2beta7GO2PROBE0.0360.0000.036
hgu2beta7GRIF0.0480.0000.047
hgu2beta7LOCUSID0.0320.0000.032
hgu2beta7MAP0.0280.0000.028
hgu2beta7OMIM0.0360.0040.038
hgu2beta7ORGANISM0.0000.0000.001
hgu2beta7PATH0.1880.0000.190
hgu2beta7PATH2PROBE0.0040.0000.003
hgu2beta7PMID0.0800.0040.081
hgu2beta7PMID2PROBE0.5840.0080.591
hgu2beta7REFSEQ0.1480.0000.146
hgu2beta7SUMFUNC0.1480.0120.161
hgu2beta7SYMBOL0.1520.0000.153
hgu2beta7UNIGENE0.0920.0000.090