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This page was generated on 2022-01-21 13:07:13 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for TFutils on tokay2


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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1949/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFutils 1.14.0  (landing page)
Vincent Carey
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 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 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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: 2022-01-21 03:57:55 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 04:04:49 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 414.2 seconds
RetCode: 0
Status:   OK  
CheckDir: TFutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TFutils.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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     27.11   1.23   28.35
tffamCirc.prep     20.45   0.00   20.45
topTraitsOfTargets  7.91   0.14    8.05
fimo16              6.71   0.67    7.38
genemodForGviz      5.83   0.91    6.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
tffamCirc.plot     26.17   0.19   26.36
tffamCirc.prep     20.49   0.06   20.55
topTraitsOfTargets  7.50   0.26    7.76
fimo16              6.93   0.25    7.17
genemodForGviz      6.25   0.34    6.60
* 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.



Installation output

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
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 22 4313k   22  980k    0     0  1686k      0  0:00:02 --:--:--  0:00:02 1685k
 92 4313k   92 4002k    0     0  2575k      0  0:00:01  0:00:01 --:--:-- 2575k
100 4313k  100 4313k    0     0  2597k      0  0:00:01  0:00:01 --:--:-- 2598k

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

Tests output

TFutils.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 
  12.70    1.25   13.93 

TFutils.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 
  17.34    0.65   18.00 

Example timings

TFutils.Rcheck/examples_i386/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog0.150.030.17
TFtargs000
URL_s3_tf000
anchor_pmids0.020.000.01
browse_gotf_main000
browse_humantfs_main000
browse_lambert_gwaslinks000
browse_lambert_main000
cisbpTFcat0.030.000.04
cisbpTFcat_2.00.050.000.05
defaultCircosParms0.020.000.01
demo_fimo_granges0.010.000.02
directHitsInCISBP0.100.000.09
encode6900.040.000.05
fimo166.710.677.38
fimoMap000
fimo_granges000
genemodForGviz5.830.916.95
genemodelDF0.090.000.10
get_rslocs_38000
grabTab0.160.000.15
gwascat_hg19_chr170.060.000.07
hocomoco.mono0.020.000.01
hocomoco.mono.sep2018000
importFIMO0.040.030.08
importFIMO_local_split0.020.010.03
lambert_snps0.250.000.25
metadata_tf000
named_tf000
retrieve_gotf_main000
retrieve_humantfs_main000
retrieve_lambert_main000
seqinfo_hg19_chr170.000.020.01
tffamCirc.plot27.11 1.2328.35
tffamCirc.prep20.45 0.0020.45
tfhash0.630.170.80
tftColl0.230.000.23
tftCollMap000
topTraitsOfTargets7.910.148.05

TFutils.Rcheck/examples_x64/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog0.180.010.18
TFtargs000
URL_s3_tf000
anchor_pmids0.010.000.02
browse_gotf_main000
browse_humantfs_main000
browse_lambert_gwaslinks000
browse_lambert_main000
cisbpTFcat0.030.000.03
cisbpTFcat_2.00.050.000.05
defaultCircosParms0.030.000.03
demo_fimo_granges000
directHitsInCISBP0.100.020.11
encode6900.680.000.69
fimo166.930.257.17
fimoMap000
fimo_granges000
genemodForGviz6.250.346.60
genemodelDF0.090.000.09
get_rslocs_38000
grabTab0.150.020.16
gwascat_hg19_chr170.030.030.06
hocomoco.mono000
hocomoco.mono.sep20180.010.000.02
importFIMO0.050.000.04
importFIMO_local_split0.010.000.02
lambert_snps0.110.060.17
metadata_tf000
named_tf000
retrieve_gotf_main000
retrieve_humantfs_main000
retrieve_lambert_main000
seqinfo_hg19_chr17000
tffamCirc.plot26.17 0.1926.36
tffamCirc.prep20.49 0.0620.55
tfhash0.320.190.51
tftColl0.160.000.16
tftCollMap000
topTraitsOfTargets7.500.267.76