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CHECK report for hgu2beta7 on riesling1

This page was generated on 2021-01-14 15:59:08 -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: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hgu2beta7.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hgu2beta7_1.31.0.tar.gz
StartedAt: 2021-01-14 11:23:01 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:23:26 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 25.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: hgu2beta7.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hgu2beta7.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings hgu2beta7_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/hgu2beta7.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'hgu2beta7' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/hgu2beta7.Rcheck/00check.log'
for details.



Installation output

hgu2beta7.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/hgu2beta7_1.31.0.tar.gz && rm -rf hgu2beta7.buildbin-libdir && mkdir hgu2beta7.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hgu2beta7.buildbin-libdir hgu2beta7_1.31.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL hgu2beta7_1.31.0.zip && rm hgu2beta7_1.31.0.tar.gz hgu2beta7_1.31.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 6561k    0  1215    0     0   1622      0  1:09:02 --:--:--  1:09:02  1620
100 6561k  100 6561k    0     0  7070k      0 --:--:-- --:--:-- --:--:-- 7070k

install for i386

* 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
  converting help for package 'hgu2beta7'
    finding HTML links ... done
    hgu2beta7                               html  
REDIRECT:topic	 hgu2beta7 -> hgu2beta7.html [ SUCCESS ]
    hgu2beta7ACCNUM                         html  
REDIRECT:topic	 hgu2beta7ACCNUM -> hgu2beta7ACCNUM.html [ SUCCESS ]
    hgu2beta7CHR                            html  
REDIRECT:topic	 hgu2beta7CHR -> hgu2beta7CHR.html [ SUCCESS ]
    hgu2beta7CHRLENGTHS                     html  
REDIRECT:topic	 hgu2beta7CHRLENGTHS -> hgu2beta7CHRLENGTHS.html [ SUCCESS ]
    hgu2beta7CHRLOC                         html  
REDIRECT:topic	 hgu2beta7CHRLOC -> hgu2beta7CHRLOC.html [ SUCCESS ]
    hgu2beta7ENZYME                         html  
REDIRECT:topic	 hgu2beta7ENZYME -> hgu2beta7ENZYME.html [ SUCCESS ]
    hgu2beta7ENZYME2PROBE                   html  
REDIRECT:topic	 hgu2beta7ENZYME2PROBE -> hgu2beta7ENZYME2PROBE.html [ SUCCESS ]
    hgu2beta7GENENAME                       html  
REDIRECT:topic	 hgu2beta7GENENAME -> hgu2beta7GENENAME.html [ SUCCESS ]
    hgu2beta7GO                             html  
REDIRECT:topic	 hgu2beta7GO -> hgu2beta7GO.html [ SUCCESS ]
    hgu2beta7GO2ALLPROBES                   html  
REDIRECT:topic	 hgu2beta7GO2ALLPROBES -> hgu2beta7GO2ALLPROBES.html [ SUCCESS ]
    hgu2beta7GO2PROBE                       html  
REDIRECT:topic	 hgu2beta7GO2PROBE -> hgu2beta7GO2PROBE.html [ SUCCESS ]
    hgu2beta7GRIF                           html  
REDIRECT:topic	 hgu2beta7GRIF -> hgu2beta7GRIF.html [ SUCCESS ]
    hgu2beta7LOCUSID                        html  
REDIRECT:topic	 hgu2beta7LOCUSID -> hgu2beta7LOCUSID.html [ SUCCESS ]
    hgu2beta7MAP                            html  
REDIRECT:topic	 hgu2beta7MAP -> hgu2beta7MAP.html [ SUCCESS ]
    hgu2beta7OMIM                           html  
REDIRECT:topic	 hgu2beta7OMIM -> hgu2beta7OMIM.html [ SUCCESS ]
    hgu2beta7ORGANISM                       html  
REDIRECT:topic	 hgu2beta7ORGANISM -> hgu2beta7ORGANISM.html [ SUCCESS ]
    hgu2beta7PATH                           html  
REDIRECT:topic	 hgu2beta7PATH -> hgu2beta7PATH.html [ SUCCESS ]
    hgu2beta7PATH2PROBE                     html  
REDIRECT:topic	 hgu2beta7PATH2PROBE -> hgu2beta7PATH2PROBE.html [ SUCCESS ]
    hgu2beta7PMID                           html  
REDIRECT:topic	 hgu2beta7PMID -> hgu2beta7PMID.html [ SUCCESS ]
    hgu2beta7PMID2PROBE                     html  
REDIRECT:topic	 hgu2beta7PMID2PROBE -> hgu2beta7PMID2PROBE.html [ SUCCESS ]
    hgu2beta7QC                             html  
REDIRECT:topic	 hgu2beta7QC -> hgu2beta7QC.html [ SUCCESS ]
REDIRECT:topic	 hgu2beta7MAPCOUNTS -> hgu2beta7QC.html [ SUCCESS ]
    hgu2beta7REFSEQ                         html  
REDIRECT:topic	 hgu2beta7REFSEQ -> hgu2beta7REFSEQ.html [ SUCCESS ]
    hgu2beta7SUMFUNC                        html  
REDIRECT:topic	 hgu2beta7SUMFUNC -> hgu2beta7SUMFUNC.html [ SUCCESS ]
    hgu2beta7SYMBOL                         html  
REDIRECT:topic	 hgu2beta7SYMBOL -> hgu2beta7SYMBOL.html [ SUCCESS ]
    hgu2beta7UNIGENE                        html  
REDIRECT:topic	 hgu2beta7UNIGENE -> hgu2beta7UNIGENE.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'hgu2beta7' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hgu2beta7' as hgu2beta7_1.31.0.zip
* DONE (hgu2beta7)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'hgu2beta7' successfully unpacked and MD5 sums checked

Tests output


Example timings

hgu2beta7.Rcheck/examples_i386/hgu2beta7-Ex.timings

nameusersystemelapsed
hgu2beta7ACCNUM0.070.020.08
hgu2beta7CHR0.010.000.02
hgu2beta7CHRLENGTHS000
hgu2beta7CHRLOC0.070.000.08
hgu2beta7ENZYME0.020.000.01
hgu2beta7ENZYME2PROBE000
hgu2beta7GENENAME0.020.000.01
hgu2beta7GO0.140.000.14
hgu2beta7GO2ALLPROBES0.120.000.13
hgu2beta7GO2PROBE0.020.000.02
hgu2beta7GRIF0.010.000.01
hgu2beta7LOCUSID0.020.000.02
hgu2beta7MAP0.010.000.01
hgu2beta7OMIM0.130.000.12
hgu2beta7ORGANISM000
hgu2beta7PATH0.010.000.01
hgu2beta7PATH2PROBE000
hgu2beta7PMID0.070.000.07
hgu2beta7PMID2PROBE0.140.000.14
hgu2beta7REFSEQ0.060.000.06
hgu2beta7SUMFUNC0.030.010.05
hgu2beta7SYMBOL0.050.020.06
hgu2beta7UNIGENE0.010.000.02

hgu2beta7.Rcheck/examples_x64/hgu2beta7-Ex.timings

nameusersystemelapsed
hgu2beta7ACCNUM0.040.010.07
hgu2beta7CHR0.020.000.02
hgu2beta7CHRLENGTHS000
hgu2beta7CHRLOC0.090.000.09
hgu2beta7ENZYME0.020.000.02
hgu2beta7ENZYME2PROBE000
hgu2beta7GENENAME0.020.020.03
hgu2beta7GO0.120.000.13
hgu2beta7GO2ALLPROBES0.110.010.12
hgu2beta7GO2PROBE0.030.000.04
hgu2beta7GRIF0.020.000.01
hgu2beta7LOCUSID0.010.000.02
hgu2beta7MAP0.070.020.07
hgu2beta7OMIM0.100.000.11
hgu2beta7ORGANISM000
hgu2beta7PATH0.020.000.02
hgu2beta7PATH2PROBE000
hgu2beta7PMID0.050.000.05
hgu2beta7PMID2PROBE0.140.000.14
hgu2beta7REFSEQ0.080.020.09
hgu2beta7SUMFUNC0.010.030.05
hgu2beta7SYMBOL0.020.000.01
hgu2beta7UNIGENE0.030.000.03