Shweta Gopaulakrishnan
| Snapshot Date: 2019-08-11 17:00:44 -0400 (Sun, 11 Aug 2019) |
| URL: https://git.bioconductor.org/packages/TFutils |
| Branch: master |
| Last Commit: 8ff90f9 |
| Last Changed Date: 2019-07-10 15:40:47 -0400 (Wed, 10 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2019-08-12 12:17:52 -0400 (Mon, 12 Aug 2019).
| Package 1649/1749 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFutils 1.5.7 Shweta Gopaulakrishnan
| malbec1 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: TFutils |
| Version: 1.5.7 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TFutils_1.5.7.tar.gz |
| StartedAt: 2019-08-12 05:23:34 -0400 (Mon, 12 Aug 2019) |
| EndedAt: 2019-08-12 05:29:46 -0400 (Mon, 12 Aug 2019) |
| EllapsedTime: 371.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFutils.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TFutils_1.5.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TFutils.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFutils/DESCRIPTION' ... OK
* this is package 'TFutils' version '1.5.7'
* 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 whether package 'TFutils' can be installed ... OK
* checking installed package size ... OK
* 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
* 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
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
'scanTabix'
fimo_granges : <anonymous>: no visible global function definition for
'seqinfo<-'
fimo_granges : <anonymous>: no visible global function definition for
'seqinfo'
fimo_granges_OLD: no visible global function definition for
'rowRanges<-'
fimo_granges_OLD : nfun : <anonymous>: no visible global function
definition for 'read.delim'
fimo_granges_OLD: no visible global function definition for
'reduceByRange'
fimo_granges_OLD : <anonymous>: no visible global function definition
for 'scanTabix'
fimo_granges_OLD : <anonymous>: no visible global function definition
for 'seqinfo<-'
fimo_granges_OLD : <anonymous>: no visible global function definition
for 'seqinfo'
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
'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 TF family
TFfamily Transcription factor cisbpTFcat geneIdType geneIds
mapIdentifiers mcols read.delim reduceByRange rowRanges<- scanTabix
seqinfo seqinfo<-
Consider adding
importFrom("base", "factor")
importFrom("stats", "family")
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' ... NOTE
Files named as vignettes but with no recognized vignette engine:
'vignettes/TFutils.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
tffamCirc.plot 23.14 1.19 24.35
tffamCirc.prep 15.30 0.00 15.29
fimo16 8.83 0.66 9.48
topTraitsOfTargets 8.05 0.40 8.46
genemodForGviz 7.25 0.95 8.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
tffamCirc.plot 29.06 0.13 29.20
tffamCirc.prep 17.25 0.00 17.26
topTraitsOfTargets 9.00 0.38 9.38
genemodForGviz 8.75 0.20 9.11
fimo16 7.73 0.30 8.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/TFutils.Rcheck/00check.log'
for details.
TFutils.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TFutils_1.5.7.tar.gz && rm -rf TFutils.buildbin-libdir && mkdir TFutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFutils.buildbin-libdir TFutils_1.5.7.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TFutils_1.5.7.zip && rm TFutils_1.5.7.tar.gz TFutils_1.5.7.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2113k 100 2113k 0 0 12.9M 0 --:--:-- --:--:-- --:--:-- 13.2M
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* 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
converting help for package 'TFutils'
finding HTML links ... done
HGNCmap html
TFCatalog-class html
TFCatalog html
TFtargs html
URL_s3_tf html
cisbpTFcat html
defaultCircosParms html
demo_fimo_granges html
directHitsInCISBP html
encode690 html
fimo16 html
fimoMap html
fimo_granges html
genemodForGviz html
genemodelDF html
grabTab html
gwascat_hg19_chr17 html
hocomoco.mono html
hocomoco.mono.sep2018 html
importFIMO html
importFIMO_local_split html
metadata_tf html
named_tf html
seqinfo_hg19_chr17 html
setupHIZE html
show-TFCatalog-method html
tffamCirc.plot html
tffamCirc.prep html
tfhash html
tftColl html
tftCollMap html
topTraitsOfTargets html
** 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
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'TFutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFutils' as TFutils_1.5.7.zip
* DONE (TFutils)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TFutils' successfully unpacked and MD5 sums checked
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TFutils.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
16.18 1.23 17.43
|
TFutils.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
17.87 0.81 18.71
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TFutils.Rcheck/examples_i386/TFutils-Ex.timings
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TFutils.Rcheck/examples_x64/TFutils-Ex.timings
|