Shweta Gopaulakrishnan
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TFutils |
| Branch: RELEASE_3_10 |
| Last Commit: 7ae9a5f |
| Last Changed Date: 2019-10-29 13:11:07 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:14:04 -0400 (Wed, 15 Apr 2020).
| Package 1720/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFutils 1.6.0 Shweta Gopaulakrishnan
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: TFutils |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TFutils_1.6.0.tar.gz |
| StartedAt: 2020-04-15 05:40:00 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:44:51 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 291.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TFutils.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TFutils.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TFutils_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/TFutils.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TFutils/DESCRIPTION’ ... OK
* this is package ‘TFutils’ version ‘1.6.0’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 3.5Mb
lambert 1.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Rsamtools’
A package should be listed in only one of these fields.
* 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 ... WARNING
'::' or ':::' imports not declared from:
'BiocFileCache' 'DT' 'httr' 'readxl' 'rjson'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
browse_lambert_gwaslinks: no visible global function definition for
‘read.csv’
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’
fimo_granges: no visible global function definition for ‘rowRanges<-’
fimo_granges : proctext: no visible global function definition for
‘read.delim’
fimo_granges: no visible global function definition for ‘reduceByRange’
fimo_granges : <anonymous>: no visible global function definition for
‘seqinfo<-’
retrieve_lambert_main: no visible global function definition for
‘bfcadd’
setupHIZE: no visible global function definition for ‘read.delim’
tffamCirc.prep: no visible binding for global variable ‘TF family’
tffamCirc.prep: no visible binding for global variable ‘TFfamily’
tffamCirc.prep: no visible binding for global variable ‘Transcription
factor’
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 TF family TFfamily
Transcription factor bfcadd cisbpTFcat mcols read.csv read.delim
reduceByRange rowRanges<- seqinfo<-
Consider adding
importFrom("base", "factor")
importFrom("stats", "family")
importFrom("utils", "read.csv", "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
tffamCirc.plot 25.668 0.236 26.043
tffamCirc.prep 15.148 0.012 15.196
topTraitsOfTargets 9.368 0.076 9.465
fimo16 8.804 0.368 9.248
genemodForGviz 7.368 0.132 7.813
get_rslocs_38 0.168 0.008 5.315
* 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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/TFutils.Rcheck/00check.log’
for details.
TFutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TFutils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘TFutils’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
17.364 0.588 18.063
TFutils.Rcheck/TFutils-Ex.timings
| name | user | system | elapsed | |
| HGNCmap | 0.000 | 0.000 | 0.001 | |
| TFCatalog | 0.672 | 0.008 | 0.681 | |
| TFtargs | 0 | 0 | 0 | |
| URL_s3_tf | 0.000 | 0.000 | 0.001 | |
| anchor_pmids | 0.008 | 0.000 | 0.007 | |
| browse_lambert_gwaslinks | 0 | 0 | 0 | |
| browse_lambert_main | 0 | 0 | 0 | |
| cisbpTFcat | 0.056 | 0.004 | 0.063 | |
| cisbpTFcat_2.0 | 0.068 | 0.004 | 0.074 | |
| defaultCircosParms | 0.012 | 0.000 | 0.012 | |
| demo_fimo_granges | 0.02 | 0.00 | 0.02 | |
| directHitsInCISBP | 0.116 | 0.004 | 0.121 | |
| encode690 | 0.060 | 0.000 | 0.059 | |
| fimo16 | 8.804 | 0.368 | 9.248 | |
| fimoMap | 0.004 | 0.000 | 0.003 | |
| fimo_granges | 0.004 | 0.000 | 0.001 | |
| genemodForGviz | 7.368 | 0.132 | 7.813 | |
| genemodelDF | 0.144 | 0.008 | 0.179 | |
| get_rslocs_38 | 0.168 | 0.008 | 5.315 | |
| grabTab | 0.340 | 0.028 | 0.367 | |
| gwascat_hg19_chr17 | 0.068 | 0.000 | 0.067 | |
| hocomoco.mono | 0.004 | 0.000 | 0.005 | |
| hocomoco.mono.sep2018 | 0.008 | 0.000 | 0.005 | |
| importFIMO | 0.040 | 0.008 | 0.061 | |
| importFIMO_local_split | 0.020 | 0.000 | 0.032 | |
| lambert_snps | 0.304 | 0.016 | 0.320 | |
| metadata_tf | 0.016 | 0.000 | 0.019 | |
| named_tf | 0.004 | 0.008 | 0.013 | |
| retrieve_lambert_main | 0 | 0 | 0 | |
| seqinfo_hg19_chr17 | 0.004 | 0.000 | 0.004 | |
| tffamCirc.plot | 25.668 | 0.236 | 26.043 | |
| tffamCirc.prep | 15.148 | 0.012 | 15.196 | |
| tfhash | 0.552 | 0.200 | 0.754 | |
| tftColl | 0.308 | 0.000 | 0.311 | |
| tftCollMap | 0.004 | 0.000 | 0.001 | |
| topTraitsOfTargets | 9.368 | 0.076 | 9.465 | |