Vincent Carey
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/TFutils |
| git_branch: RELEASE_3_14 |
| git_last_commit: 3c4cda1 |
| git_last_commit_date: 2021-10-26 12:43:41 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:28 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the TFutils package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFutils.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1949/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TFutils 1.14.0 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: TFutils |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TFutils_1.14.0.tar.gz |
| StartedAt: 2022-04-13 04:00:49 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 04:07:52 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 422.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TFutils.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TFutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TFutils_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TFutils.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.14.0'
* 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 ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 3.5Mb
lambert 1.4Mb
* 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
* 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
fimo_granges : proctext: warning in read.delim(con, h = FALSE,
stringsAsFactors = FALSE, sep = "\t"): partial argument match of 'h'
to 'header'
setupHIZE: warning in read.delim(txtfn, sep = "\t", skip = 3, h =
FALSE, stringsAsFactors = FALSE): partial argument match of 'h' to
'header'
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: no visible global function definition for 'reduceByRange'
fimo_granges : <anonymous>: no visible global function definition for
'seqinfo<-'
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 cisbpTFcat mcols reduceByRange rowRanges<-
seqinfo<-
Consider adding
importFrom("base", "factor")
importFrom("stats", "family")
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 LazyData ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tffamCirc.plot 25.76 0.84 26.61
tffamCirc.prep 17.93 0.00 17.93
topTraitsOfTargets 7.60 0.30 7.89
genemodForGviz 6.47 0.72 7.36
fimo16 5.97 0.61 6.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tffamCirc.plot 28.62 0.20 28.83
tffamCirc.prep 21.35 0.00 21.34
topTraitsOfTargets 8.23 0.42 8.65
fimo16 6.77 0.32 7.08
genemodForGviz 5.97 0.43 6.41
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/TFutils.Rcheck/00check.log'
for details.
TFutils.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/TFutils_1.14.0.tar.gz && rm -rf TFutils.buildbin-libdir && mkdir TFutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFutils.buildbin-libdir TFutils_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL TFutils_1.14.0.zip && rm TFutils_1.14.0.tar.gz TFutils_1.14.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
52 4313k 52 2267k 0 0 2178k 0 0:00:01 0:00:01 --:--:-- 2178k
100 4313k 100 4313k 0 0 2600k 0 0:00:01 0:00:01 --:--:-- 2599k
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'TFutils/vignettes/TFutils_f1000/TFutils.Rmd' to 'TFutils/vignettes/TFutils.Rmd'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'TFutils/vignettes/TFutils_f1000/f1000_styles.sty' to 'TFutils/vignettes/f1000_styles.sty'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'TFutils/vignettes/TFutils_f1000/AMIGOplus.png' to 'TFutils/vignettes/AMIGOplus.png'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'TFutils/vignettes/TFutils_f1000/F1000header.png' to 'TFutils/vignettes/F1000header.png'
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
anchor_pmids html
browse_gotf_main html
browse_humantfs_main html
browse_lambert_gwaslinks html
browse_lambert_main html
cisbpTFcat html
cisbpTFcat_2.0 html
defaultCircosParms html
demo_fimo_granges html
directHitsInCISBP html
encode690 html
fimo16 html
fimoMap html
fimo_granges html
genemodForGviz html
genemodelDF html
get_rslocs_38 html
grabTab html
gwascat_hg19_chr17 html
hocomoco.mono html
hocomoco.mono.sep2018 html
importFIMO html
importFIMO_local_split html
lambert_snps html
metadata_tf html
named_tf html
retrieve_gotf_main html
retrieve_humantfs_main html
retrieve_lambert_main 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) :
failed to copy 'TFutils/vignettes/TFutils_f1000/TFutils.Rmd' to 'TFutils/vignettes/TFutils.Rmd'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'TFutils/vignettes/TFutils_f1000/f1000_styles.sty' to 'TFutils/vignettes/f1000_styles.sty'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'TFutils/vignettes/TFutils_f1000/AMIGOplus.png' to 'TFutils/vignettes/AMIGOplus.png'
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'TFutils/vignettes/TFutils_f1000/F1000header.png' to 'TFutils/vignettes/F1000header.png'
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_1.14.0.zip
* DONE (TFutils)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'TFutils' successfully unpacked and MD5 sums checked
|
TFutils.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
>
>
> proc.time()
user system elapsed
13.09 1.06 14.12
|
TFutils.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
>
>
> proc.time()
user system elapsed
13.39 0.71 14.09
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TFutils.Rcheck/examples_i386/TFutils-Ex.timings
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TFutils.Rcheck/examples_x64/TFutils-Ex.timings
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