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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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 1388/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NeuCA 1.11.0  (landing page)
Hao Feng
Snapshot Date: 2024-06-14 14:00 -0400 (Fri, 14 Jun 2024)
git_url: https://git.bioconductor.org/packages/NeuCA
git_branch: devel
git_last_commit: 06cc722
git_last_commit_date: 2024-04-30 11:35:52 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for NeuCA on nebbiolo2

To the developers/maintainers of the NeuCA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NeuCA.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: NeuCA
Version: 1.11.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:NeuCA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings NeuCA_1.11.0.tar.gz
StartedAt: 2024-06-15 01:29:36 -0400 (Sat, 15 Jun 2024)
EndedAt: 2024-06-15 01:33:09 -0400 (Sat, 15 Jun 2024)
EllapsedTime: 212.4 seconds
RetCode: 0
Status:   OK  
CheckDir: NeuCA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:NeuCA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings NeuCA_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/NeuCA.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘NeuCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NeuCA’ version ‘1.11.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘NeuCA’ 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 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 loading without being on the library search path ... 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
HNN_assign: no visible global function definition for ‘txtProgressBar’
HNN_assign: no visible global function definition for
  ‘setTxtProgressBar’
HNN_assign: no visible global function definition for ‘predict’
NeuCA: no visible global function definition for ‘is’
NeuCA: no visible global function definition for ‘assay’
NeuCA: no visible global function definition for ‘predict’
SCHwrapper: no visible binding for global variable ‘sd’
SampleNorm: no visible binding for global variable ‘sd’
assignCT: no visible global function definition for ‘na.omit’
cor.det: no visible global function definition for ‘cor’
train_SCH: no visible global function definition for ‘na.omit’
train_SCH: no visible global function definition for ‘dist’
train_SCH: no visible global function definition for ‘hclust’
Undefined global functions or variables:
  assay cor dist hclust is na.omit predict sd setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "cor", "dist", "hclust", "na.omit", "predict",
             "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
NeuCA 14.426  1.603  12.464
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/NeuCA.Rcheck/00check.log’
for details.


Installation output

NeuCA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL NeuCA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘NeuCA’ ...
** using staged installation
** R
** data
** 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 (NeuCA)

Tests output


Example timings

NeuCA.Rcheck/NeuCA-Ex.timings

nameusersystemelapsed
Baron_counts0.2230.0440.266
NeuCA14.426 1.60312.464
Seg_counts0.2750.0000.274