ENCODExplorer 2.2.0
Charles Joly Beauparlant
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ENCODExplorer | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ENCODExplorer_2.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ENCODExplorer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENCODExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorer’ version ‘2.2.0’
* 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 ‘ENCODExplorer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 73.6Mb
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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createDesign 6.024 1.20 7.225
searchToquery 3.192 0.68 6.335
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/home/biocbuild/bbs-3.5-bioc/meat/ENCODExplorer.Rcheck/00check.log’
for details.
* 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
* DONE (ENCODExplorer)