Shweta Gopaulakrishnan
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/TFutils |
| Branch: RELEASE_3_9 |
| Last Commit: a2f8f46 |
| Last Changed Date: 2019-05-02 11:54:11 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:41:08 -0400 (Wed, 16 Oct 2019).
| Package 1643/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TFutils 1.4.0 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 | |
| Package: TFutils |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TFutils_1.4.0.tar.gz |
| StartedAt: 2019-10-16 07:32:30 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:36:03 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 212.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TFutils.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TFutils_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-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 '1.4.0'
* 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 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 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TFutils.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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
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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
'AMIGO.png', 'AMIGOplus.png', 'F1000header.png', 'README.txt',
'TFutils.Rmd', 'TFutils_f1000/AMIGO.png',
'TFutils_f1000/AMIGOplus.png', 'TFutils_f1000/F1000header.png',
'TFutils_f1000/Makefile', 'TFutils_f1000/TFutils.Rmd',
'TFutils_f1000/f1000_styles.sty', 'TFutils_f1000/ormdl3CEBPB.png',
'TFutils_f1000/tfTargsApp.png', 'TFutils_f1000/tfsrcs.bib',
'f1000_styles.sty', 'ormdl3CEBPB.png', 'tfTargsApp.png',
'tfsrcs.bib'
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
topTraitsOfTargets 7.00 0.35 7.34
fimo16 6.16 0.76 6.92
genemodForGviz 5.61 0.69 6.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topTraitsOfTargets 8.19 0.47 8.65
fimo16 8.16 0.42 8.58
genemodForGviz 5.76 0.27 6.03
* 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 PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TFutils_1.4.0.tar.gz && rm -rf TFutils.buildbin-libdir && mkdir TFutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFutils.buildbin-libdir TFutils_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TFutils_1.4.0.zip && rm TFutils_1.4.0.tar.gz TFutils_1.4.0.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 2106k 100 2106k 0 0 7864k 0 --:--:-- --:--:-- --:--:-- 8041k
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
Warning: in method for 'importFIMO' with signature '"TabixFile","GRanges"': no definition for classes "TabixFile", "GRanges"
** 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
directHitsInCISBP html
encode690 html
fimo16 html
fimoMap 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
setupHIZE html
show-TFCatalog-method 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_1.4.0.zip
* DONE (TFutils)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TFutils' successfully unpacked and MD5 sums checked
|
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
12.92 1.06 13.96
|
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
18.68 0.90 19.65
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TFutils.Rcheck/examples_i386/TFutils-Ex.timings
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TFutils.Rcheck/examples_x64/TFutils-Ex.timings
|