Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-06-17 11:38:16 -0400 (Sat, 17 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-18 r84287) -- "Already Tomorrow" 4599
palomino4Windows Server 2022 Datacenterx644.3.0 RC (2023-04-18 r84287 ucrt) -- "Already Tomorrow" 4349
lconwaymacOS 12.6.5 Montereyx86_644.3.0 RC (2023-04-13 r84266) -- "Already Tomorrow" 4356
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4381
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 603/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.35.0  (landing page)
Ning Leng
Snapshot Date: 2023-06-16 14:00:07 -0400 (Fri, 16 Jun 2023)
git_url: https://git.bioconductor.org/packages/EBSeqHMM
git_branch: devel
git_last_commit: 6a6283d
git_last_commit_date: 2023-04-25 10:36:24 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for EBSeqHMM on lconway


The builds on kunpeng2 (Linux ARM64) are experimental!
To the developers/maintainers of the EBSeqHMM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBSeqHMM.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: EBSeqHMM
Version: 1.35.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeqHMM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeqHMM_1.35.0.tar.gz
StartedAt: 2023-06-16 19:50:25 -0400 (Fri, 16 Jun 2023)
EndedAt: 2023-06-16 19:51:30 -0400 (Fri, 16 Jun 2023)
EllapsedTime: 65.4 seconds
RetCode: 0
Status:   OK  
CheckDir: EBSeqHMM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeqHMM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeqHMM_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/EBSeqHMM.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBSeqHMM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeqHMM’ version ‘1.35.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘EBSeqHMM’ can be installed ... OK
* 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 ... OK
* checking R 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 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
EBHMMNBfun: no visible binding for global variable ‘median’
EBHMMNBfun : <anonymous>: no visible global function definition for
  ‘quantile’
EBHMMNBfun: no visible global function definition for ‘optim’
EBHMMNBfunForMulti: no visible binding for global variable ‘median’
EBHMMNBfunForMulti : <anonymous>: no visible global function definition
  for ‘quantile’
EBHMMNBfunForMulti: no visible global function definition for ‘optim’
EBSeqHMMTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBTest_ext: no visible global function definition for ‘quantile’
EBTest_ext: no visible binding for global variable ‘var’
PlotExp: no visible global function definition for ‘axis’
PlotExp : <anonymous>: no visible global function definition for
  ‘median’
PlotExp: no visible global function definition for ‘lines’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
  axis lines median optim quantile var
Consider adding
  importFrom("graphics", "axis", "lines")
  importFrom("stats", "median", "optim", "quantile", "var")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/EBSeqHMM.Rcheck/00check.log’
for details.



Installation output

EBSeqHMM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EBSeqHMM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘EBSeqHMM’ ...
** using staged installation
** R
** data
** demo
** 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 (EBSeqHMM)

Tests output


Example timings

EBSeqHMM.Rcheck/EBSeqHMM-Ex.timings

nameusersystemelapsed
EBHMMNBMultiEM_2chain0.5560.0190.577
EBHMMNBfun0.0530.0020.055
EBHMMNBfunForMulti0.2230.0120.236
EBSeqHMM-package0.5070.0090.518
EBSeqHMMTest0.5400.0090.550
EBTest_ext0.1450.0040.150
GeneExampleData0.0070.0010.009
GetAllPaths0.5530.0070.562
GetConfidentCalls0.4610.0070.470
GetDECalls0.5070.0050.514
IsoExampleList0.0130.0020.016
LikefunNBHMM0.0060.0010.008
PlotExp0.0050.0020.007
beta.mom000
f00.0000.0010.001