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CHECK report for ELMER.data on riesling1

This page was generated on 2021-01-21 16:01:27 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE ELMER.data PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 111/386HostnameOS / ArchINSTALLBUILDCHECK
ELMER.data 2.15.0
Tiago Chedraoui Silva
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/ELMER.data
Branch: master
Last Commit: 25cce04
Last Changed Date: 2020-10-27 10:13:21 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: ELMER.data
Version: 2.15.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ELMER.data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ELMER.data_2.15.0.tar.gz
StartedAt: 2021-01-21 11:21:46 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:24:59 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 193.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ELMER.data.Rcheck
Warnings: 0

Command output

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##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ELMER.data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ELMER.data_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/ELMER.data.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 'ELMER.data/DESCRIPTION' ... OK
* this is package 'ELMER.data' version '2.15.0'
* 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:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ELMER.data' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 293.1Mb
  sub-directories of 1Mb or more:
    data  292.9Mb
* checking package directory ... OK
* checking 'build' 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
* 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 ... OK
* 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
  Note: found 36 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/ELMER.data.Rcheck/00check.log'
for details.



Installation output

ELMER.data.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/ELMER.data_2.15.0.tar.gz && rm -rf ELMER.data.buildbin-libdir && mkdir ELMER.data.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ELMER.data.buildbin-libdir ELMER.data_2.15.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ELMER.data_2.15.0.zip && rm ELMER.data_2.15.0.tar.gz ELMER.data_2.15.0.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
 12  292M   12 37.5M    0     0  42.5M      0  0:00:06 --:--:--  0:00:06 42.5M
 41  292M   41  122M    0     0  66.0M      0  0:00:04  0:00:01  0:00:03 66.0M
 56  292M   56  164M    0     0  57.5M      0  0:00:05  0:00:02  0:00:03 57.5M
 65  292M   65  191M    0     0  49.7M      0  0:00:05  0:00:03  0:00:02 49.7M
100  292M  100  292M    0     0  61.4M      0  0:00:04  0:00:04 --:--:-- 61.4M

install for i386

* installing *source* package 'ELMER.data' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ELMER.data'
    finding HTML links ... done
    ELMER.data                              html  
REDIRECT:topic	 ELMER.data -> ELMER.data.html [ SUCCESS ]
REDIRECT:topic	 ELMER.data-package -> ELMER.data.html [ SUCCESS ]
    EPIC.hg19.manifest                      html  
REDIRECT:topic	 EPIC.hg19.manifest -> EPIC.hg19.manifest.html [ SUCCESS ]
    EPIC.hg38.manifest                      html  
REDIRECT:topic	 EPIC.hg38.manifest -> EPIC.hg38.manifest.html [ SUCCESS ]
    GeneExp                                 html  
REDIRECT:topic	 GeneExp -> GeneExp.html [ SUCCESS ]
    Human_genes__GRCh37_p13                 html  
REDIRECT:topic	 Human_genes__GRCh37_p13 -> Human_genes__GRCh37_p13.html [ SUCCESS ]
    Human_genes__GRCh37_p13__tss            html  
REDIRECT:topic	 Human_genes__GRCh37_p13__tss -> Human_genes__GRCh37_p13__tss.html [ SUCCESS ]
    Human_genes__GRCh38_p12                 html  
REDIRECT:topic	 Human_genes__GRCh38_p12 -> Human_genes__GRCh38_p12.html [ SUCCESS ]
    Human_genes__GRCh38_p12__tss            html  
REDIRECT:topic	 Human_genes__GRCh38_p12__tss -> Human_genes__GRCh38_p12__tss.html [ SUCCESS ]
    Meth                                    html  
REDIRECT:topic	 Meth -> Meth.html [ SUCCESS ]
    Probes.motif.hg19.450K                  html  
REDIRECT:topic	 Probes.motif.hg19.450K -> Probes.motif.hg19.450K.html [ SUCCESS ]
    Probes.motif.hg19.EPIC                  html  
REDIRECT:topic	 Probes.motif.hg19.EPIC -> Probes.motif.hg19.EPIC.html [ SUCCESS ]
    Probes.motif.hg38.450K                  html  
REDIRECT:topic	 Probes.motif.hg38.450K -> Probes.motif.hg38.450K.html [ SUCCESS ]
    Probes.motif.hg38.EPIC                  html  
REDIRECT:topic	 Probes.motif.hg38.EPIC -> Probes.motif.hg38.EPIC.html [ SUCCESS ]
    TF.family                               html  
REDIRECT:topic	 TF.family -> TF.family.html [ SUCCESS ]
    TF.subfamily                            html  
REDIRECT:topic	 TF.subfamily -> TF.subfamily.html [ SUCCESS ]
    data                                    html  
REDIRECT:topic	 data -> data.html [ SUCCESS ]
    hm450.hg19.manifest                     html  
REDIRECT:topic	 hm450.hg19.manifest -> hm450.hg19.manifest.html [ SUCCESS ]
    hm450.hg38.manifest                     html  
REDIRECT:topic	 hm450.hg38.manifest -> hm450.hg38.manifest.html [ SUCCESS ]
    hocomoco.table                          html  
REDIRECT:topic	 hocomoco.table -> hocomoco.table.html [ SUCCESS ]
    human.TF                                html  
REDIRECT:topic	 human.TF -> human.TF.html [ SUCCESS ]
    mae.promoter                            html  
REDIRECT:topic	 mae.promoter -> mae.promoter.html [ SUCCESS ]
** building package indices
** installing vignettes
** 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 'ELMER.data' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ELMER.data' as ELMER.data_2.15.0.zip
* DONE (ELMER.data)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'ELMER.data' successfully unpacked and MD5 sums checked

Tests output


Example timings

ELMER.data.Rcheck/examples_i386/ELMER.data-Ex.timings

nameusersystemelapsed
ELMER.data000
EPIC.hg19.manifest000
EPIC.hg38.manifest000
Probes.motif.hg19.450K000
Probes.motif.hg19.EPIC000
Probes.motif.hg38.450K000
Probes.motif.hg38.EPIC000
data000
hm450.hg19.manifest000
hm450.hg38.manifest000
mae.promoter000

ELMER.data.Rcheck/examples_x64/ELMER.data-Ex.timings

nameusersystemelapsed
ELMER.data000
EPIC.hg19.manifest000
EPIC.hg38.manifest000
Probes.motif.hg19.450K000
Probes.motif.hg19.EPIC000
Probes.motif.hg38.450K000
Probes.motif.hg38.EPIC000
data000
hm450.hg19.manifest000
hm450.hg38.manifest000
mae.promoter000