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BioC 3.6: CHECK report for ENCODExplorer on tokay1

This page was generated on 2017-08-16 13:34:34 -0400 (Wed, 16 Aug 2017).

Package 404/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ENCODExplorer 2.3.0
Charles Joly Beauparlant
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ENCODExplorer
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ENCODExplorer
Version: 2.3.0
Command: rm -rf ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && mkdir ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.3.0.tar.gz >ENCODExplorer.Rcheck\00install.out 2>&1 && cp ENCODExplorer.Rcheck\00install.out ENCODExplorer-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ENCODExplorer.buildbin-libdir --install="check:ENCODExplorer-install.out" --force-multiarch --no-vignettes --timings ENCODExplorer_2.3.0.tar.gz
StartedAt: 2017-08-15 23:13:16 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:17:27 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 250.6 seconds
RetCode: 0
Status:  OK  
CheckDir: ENCODExplorer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && mkdir ENCODExplorer.buildbin-libdir ENCODExplorer.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENCODExplorer.buildbin-libdir ENCODExplorer_2.3.0.tar.gz >ENCODExplorer.Rcheck\00install.out 2>&1 && cp ENCODExplorer.Rcheck\00install.out ENCODExplorer-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ENCODExplorer.buildbin-libdir --install="check:ENCODExplorer-install.out" --force-multiarch --no-vignettes --timings ENCODExplorer_2.3.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ENCODExplorer.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ENCODExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENCODExplorer' version '2.3.0'
* 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 'ENCODExplorer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 73.5Mb
  sub-directories of 1Mb or more:
    data     23.9Mb
    doc       1.5Mb
    extdata  48.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
clean_column: no visible binding for global variable 'col_name'
clean_column: no visible binding for global variable 'value'
createDesign: no visible global function definition for 'data'
createDesign: no visible binding for global variable 'encode_df'
createDesign: no visible binding for global variable 'file_format'
createDesign: no visible binding for global variable 'status'
createDesign: no visible binding for global variable 'accession'
createDesign: no visible binding for global variable 'controls'
createDesign : get_ctrl_design: no visible binding for global variable
  'accession'
createDesign : get_ctrl_design: no visible binding for global variable
  'href'
createDesign: no visible global function definition for '.'
createDesign: no visible binding for global variable 'href'
createDesign: no visible binding for global variable 'Experiment'
createDesign: no visible binding for global variable 'Value'
downloadEncode: no visible global function definition for 'data'
downloadEncode: no visible binding for global variable 'encode_df'
downloadEncode: no visible binding for global variable 'file_accession'
downloadEncode: no visible binding for global variable 'file_format'
downloadEncode: no visible binding for global variable 'accession'
download_single_file: no visible global function definition for
  'download.file'
export_ENCODEdb_matrix: no visible binding for global variable
  'accession'
fuzzySearch: no visible global function definition for 'data'
queryEncode: no visible global function definition for 'data'
queryEncode: no visible binding for global variable 'encode_df'
searchToquery: no visible global function definition for 'data'
shinyEncode: no visible binding for global variable 'ui'
shinyEncode: no visible binding for global variable 'server'
step11: no visible binding for global variable 'submitted_by'
step3: no visible binding for global variable 'project'
step3: no visible binding for global variable 'platform'
step3: no visible binding for global variable 'lab'
step4: no visible binding for global variable
  'biological_replicate_number'
step4: no visible binding for global variable 'replicate_library'
step4: no visible binding for global variable 'replicate_antibody'
step4: no visible binding for global variable 'antibody_target'
step4: no visible binding for global variable
  'antibody_characterization'
step4: no visible binding for global variable 'antibody_caption'
step4: no visible binding for global variable
  'technical_replicate_number'
step4: no visible binding for global variable 'treatment'
step4: no visible binding for global variable 'nucleic_acid_term'
step6_assay: no visible binding for global variable 'assay'
step6_biosample_name: no visible binding for global variable
  'biosample_name'
step6_biosample_type: no visible binding for global variable
  'biosample_type'
step6_control: no visible binding for global variable 'controls'
step6_date_released: no visible binding for global variable
  'date_released'
step6_status: no visible binding for global variable 'status'
step6_target: no visible binding for global variable 'target'
step7: no visible binding for global variable 'organism'
step8: no visible binding for global variable 'investigated_as'
step8: no visible binding for global variable 'target'
step9: no visible binding for global variable 'organism'
Undefined global functions or variables:
  . Experiment Value accession antibody_caption
  antibody_characterization antibody_target assay
  biological_replicate_number biosample_name biosample_type col_name
  controls data date_released download.file encode_df file_accession
  file_format href investigated_as lab nucleic_acid_term organism
  platform project replicate_antibody replicate_library server status
  submitted_by target technical_replicate_number treatment ui value
Consider adding
  importFrom("utils", "data", "download.file")
to your NAMESPACE file.
* 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 771 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
createDesign  5.59   0.56    6.16
searchToquery 3.28   0.21    5.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
createDesign  6.16   0.41    6.59
searchToquery 3.09   0.21    5.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ENCODExplorer.Rcheck/00check.log'
for details.


ENCODExplorer.Rcheck/00install.out:


install for i386

* installing *source* package 'ENCODExplorer' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ENCODExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ENCODExplorer' as ENCODExplorer_2.3.0.zip
* DONE (ENCODExplorer)

ENCODExplorer.Rcheck/examples_i386/ENCODExplorer-Ex.timings:

nameusersystemelapsed
createDesign5.590.566.16
downloadEncode0.220.000.22
export_ENCODEdb_matrix000
fuzzySearch0.040.000.11
prepare_ENCODEdb1.390.332.55
queryEncode000
searchEncode0.540.012.49
searchToquery3.280.215.37
shinyEncode000

ENCODExplorer.Rcheck/examples_x64/ENCODExplorer-Ex.timings:

nameusersystemelapsed
createDesign6.160.416.59
downloadEncode0.240.000.23
export_ENCODEdb_matrix000
fuzzySearch0.050.000.17
prepare_ENCODEdb1.390.142.20
queryEncode000
searchEncode0.600.002.86
searchToquery3.090.215.47
shinyEncode000