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This page was generated on 2024-06-21 17:40 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 2143/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TEKRABber 1.8.0  (landing page)
Yao-Chung Chen
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/TEKRABber
git_branch: RELEASE_3_19
git_last_commit: a0f7fd4
git_last_commit_date: 2024-04-30 11:40:20 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    NA  


CHECK results for TEKRABber on palomino3

To the developers/maintainers of the TEKRABber package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TEKRABber.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TEKRABber
Version: 1.8.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TEKRABber.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings TEKRABber_1.8.0.tar.gz
StartedAt: 2024-06-20 13:49:14 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 14:15:05 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 1550.6 seconds
RetCode: 0
Status:   OK  
CheckDir: TEKRABber.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TEKRABber.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings TEKRABber_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/TEKRABber.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TEKRABber/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TEKRABber' version '1.8.0'
* 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 'TEKRABber' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* 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 ... NOTE
Problems with news in 'NEWS.md':
No news entries found.
* checking code 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 whether startup messages can be suppressed ... 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
File 'TEKRABber/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(paste(messages, collapse = "\n"))

See section 'Good practice' in '?.onAttach'.

appTEKRABber: no visible global function definition for 'grid_page'
appTEKRABber: no visible global function definition for
  'grid_card_text'
appTEKRABber: no visible global function definition for 'grid_card'
appTEKRABber: no visible global function definition for 'card_header'
appTEKRABber: no visible global function definition for 'card_body'
appTEKRABber: no visible global function definition for
  'selectizeInput'
appTEKRABber: no visible global function definition for 'actionButton'
appTEKRABber: no visible global function definition for 'plotlyOutput'
appTEKRABber: no visible global function definition for 'plotOutput'
appTEKRABber : server: no visible global function definition for
  'renderPlotly'
appTEKRABber : server: no visible global function definition for
  'plot_ly'
appTEKRABber : server: no visible global function definition for
  'observeEvent'
appTEKRABber : server: no visible global function definition for
  'renderPlot'
appTEKRABber : server: no visible global function definition for
  'ggplot'
appTEKRABber : server: no visible global function definition for 'aes'
appTEKRABber : server: no visible binding for global variable 'gene'
appTEKRABber : server: no visible binding for global variable 'TE'
appTEKRABber : server: no visible global function definition for
  'geom_point'
appTEKRABber : server: no visible global function definition for 'labs'
appTEKRABber : server: no visible global function definition for
  'geom_smooth'
appTEKRABber : server: no visible global function definition for
  'theme_bw'
appTEKRABber : server: no visible global function definition for
  'ggtitle'
appTEKRABber : server: no visible global function definition for
  'ggviolin'
appTEKRABber : server: no visible global function definition for 'ylab'
appTEKRABber : server: no visible global function definition for 'xlab'
appTEKRABber : server: no visible global function definition for
  'theme'
appTEKRABber: no visible global function definition for 'shinyApp'
corrOrthologTE: no visible binding for global variable 'i'
corrOrthologTE: no visible binding for global variable 'j'
corrOrthologTE: no visible global function definition for 'cor.test'
orthologScale: no visible global function definition for 'desc'
orthologScale: no visible binding for global variable
  'orthologyConfidence'
orthologScale: no visible binding for global variable 'refLength'
orthologScale: no visible binding for global variable 'compareLength'
orthologScale: no visible global function definition for 'across'
orthologScale: no visible binding for global variable 'refLen'
orthologScale: no visible binding for global variable 'compareLen'
prepareRMSK: no visible binding for global variable 'repEnd'
prepareRMSK: no visible binding for global variable 'repStart'
prepareRMSK: no visible binding for global variable 'repName'
prepareRMSK: no visible binding for global variable 'repClass'
prepareRMSK: no visible binding for global variable 'rLen'
prepareRMSK: no visible binding for global variable 'cLen'
Undefined global functions or variables:
  TE across actionButton aes cLen card_body card_header compareLen
  compareLength cor.test desc gene geom_point geom_smooth ggplot
  ggtitle ggviolin grid_card grid_card_text grid_page i j labs
  observeEvent orthologyConfidence plotOutput plot_ly plotlyOutput rLen
  refLen refLength renderPlot renderPlotly repClass repEnd repName
  repStart selectizeInput shinyApp theme theme_bw xlab ylab
Consider adding
  importFrom("stats", "cor.test")
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/TEKRABber/libs/x64/TEKRABber.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
prepareRMSK    292.74  15.91  334.19
DECorrInputs    57.79   4.95   76.97
orthologScale   55.59   2.96   73.37
corrOrthologTE  40.87   0.86   67.17
DEgeneTE        27.85   1.34   29.23
appTEKRABber    25.44   0.69   77.82
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/TEKRABber.Rcheck/00check.log'
for details.


Installation output

TEKRABber.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL TEKRABber
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'TEKRABber' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_corr.cpp -o rcpp_corr.o
rcpp_corr.cpp:23: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   23 |     #pragma omp parallel for
      | 
g++ -std=gnu++17 -shared -s -static-libgcc -o TEKRABber.dll tmp.def RcppExports.o rcpp_corr.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-TEKRABber/00new/TEKRABber/libs/x64
** R
** data
** 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 (TEKRABber)

Tests output

TEKRABber.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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("TEKRABber")
Welcome to TEKRABber version 1.8.0
+ New function: prepareRMSK() for getting repeatmasker
+ New parameter: `numCore` in corrOrthologTE() for parallel computing
> test_check("TEKRABber")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 10 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-corrOrthologTE.R:31:5'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
 156.93   23.54  214.09 

Example timings

TEKRABber.Rcheck/TEKRABber-Ex.timings

nameusersystemelapsed
DECorrInputs57.79 4.9576.97
DEgeneTE27.85 1.3429.23
appTEKRABber25.44 0.6977.82
corrOrthologTE40.87 0.8667.17
ctInputDE0.140.080.23
fetchDataHmChimp1.090.331.42
hg38_panTro6_rmsk0.070.080.15
orthologScale55.59 2.9673.37
prepareRMSK292.74 15.91334.19
speciesCounts0.350.020.37