Shweta Gopaulakrishnan
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TFutils |
| Branch: master |
| Last Commit: 5089ea9 |
| Last Changed Date: 2019-01-16 15:29:11 -0400 (Wed, 16 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:20:13 -0400 (Tue, 09 Apr 2019).
| Package 1608/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFutils 1.3.4 Shweta Gopaulakrishnan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: TFutils |
| Version: 1.3.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFutils_1.3.4.tar.gz |
| StartedAt: 2019-04-09 05:56:39 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:00:13 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 213.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TFutils.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TFutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TFutils_1.3.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TFutils/DESCRIPTION’ ... OK
* this is package ‘TFutils’ version ‘1.3.4’
* package encoding: UTF-8
* 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 ‘TFutils’ can be installed ... WARNING
Found the following significant warnings:
Warning: in method for ‘importFIMO’ with signature ‘"TabixFile","GRanges"’: no definition for classes “TabixFile”, “GRanges”
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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
directHitsInCISBP: no visible binding for global variable
‘DISEASE.TRAIT’
directHitsInCISBP: no visible binding for global variable ‘MAPPED_GENE’
directHitsInCISBP: no visible binding for global variable ‘cisbpTFcat’
directHitsInCISBP: no visible binding for global variable ‘HGNC’
directHitsInCISBP: no visible binding for global variable ‘Family_Name’
setupHIZE: no visible global function definition for ‘read.delim’
topTraitsOfTargets: no visible global function definition for
‘geneIdType’
topTraitsOfTargets: no visible global function definition for
‘mapIdentifiers’
topTraitsOfTargets: no visible global function definition for
‘SymbolIdentifier’
topTraitsOfTargets: no visible global function definition for ‘geneIds’
topTraitsOfTargets: no visible global function definition for ‘mcols’
topTraitsOfTargets: no visible binding for global variable
‘DISEASE.TRAIT’
Undefined global functions or variables:
DISEASE.TRAIT Family_Name HGNC MAPPED_GENE SymbolIdentifier
cisbpTFcat geneIdType geneIds mapIdentifiers mcols read.delim
Consider adding
importFrom("utils", "read.delim")
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 62 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topTraitsOfTargets 13.265 0.842 14.107
fimo16 12.103 0.756 12.861
genemodForGviz 8.980 0.602 9.686
TFCatalog 5.025 0.421 5.448
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck/00check.log’
for details.
TFutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TFutils ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘TFutils’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: in method for ‘importFIMO’ with signature ‘"TabixFile","GRanges"’: no definition for classes “TabixFile”, “GRanges” ** help *** installing help indices ** 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 * DONE (TFutils)
TFutils.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(TFutils)
>
> test_check("TFutils")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 5 SKIPPED: 0 FAILED: 0
>
>
> proc.time()
user system elapsed
20.270 1.693 21.917
TFutils.Rcheck/TFutils-Ex.timings
| name | user | system | elapsed | |
| HGNCmap | 0.000 | 0.001 | 0.000 | |
| TFCatalog | 5.025 | 0.421 | 5.448 | |
| TFtargs | 0 | 0 | 0 | |
| URL_s3_tf | 0.001 | 0.000 | 0.001 | |
| cisbpTFcat | 0.058 | 0.012 | 0.070 | |
| directHitsInCISBP | 1.524 | 0.087 | 1.610 | |
| encode690 | 0.102 | 0.003 | 0.104 | |
| fimo16 | 12.103 | 0.756 | 12.861 | |
| fimoMap | 0.003 | 0.001 | 0.004 | |
| genemodForGviz | 8.980 | 0.602 | 9.686 | |
| genemodelDF | 0.197 | 0.033 | 0.230 | |
| grabTab | 0.569 | 0.100 | 0.670 | |
| gwascat_hg19_chr17 | 0.081 | 0.013 | 0.094 | |
| hocomoco.mono | 0.009 | 0.002 | 0.011 | |
| hocomoco.mono.sep2018 | 0.008 | 0.002 | 0.011 | |
| importFIMO | 0.060 | 0.012 | 0.074 | |
| importFIMO_local_split | 0.026 | 0.010 | 0.037 | |
| metadata_tf | 0.029 | 0.016 | 0.045 | |
| named_tf | 0.019 | 0.018 | 0.037 | |
| tfhash | 1.757 | 0.891 | 2.648 | |
| tftColl | 0.143 | 0.021 | 0.165 | |
| tftCollMap | 0.002 | 0.000 | 0.002 | |
| topTraitsOfTargets | 13.265 | 0.842 | 14.107 | |