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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 2010/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNAGEE 1.44.0  (landing page)
David Venet
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/SNAGEE
git_branch: RELEASE_3_19
git_last_commit: 4c29a44
git_last_commit_date: 2024-04-30 10:29:34 -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 SNAGEE on palomino3

To the developers/maintainers of the SNAGEE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SNAGEE.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: SNAGEE
Version: 1.44.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNAGEE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SNAGEE_1.44.0.tar.gz
StartedAt: 2024-06-20 12:37:14 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 12:40:32 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 198.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SNAGEE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNAGEE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SNAGEE_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SNAGEE.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 'SNAGEE/DESCRIPTION' ... OK
* this is package 'SNAGEE' version '1.44.0'
* 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 whether package 'SNAGEE' 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 dependencies in R code ... NOTE
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
qualSample: no visible global function definition for 'sd'
qualSample: no visible global function definition for 'cor'
qualSample: no visible global function definition for 'mclapply'
qualSample: no visible global function definition for 'median'
qualSample: no visible global function definition for 'mad'
qualStudy: no visible global function definition for 'cor'
qualStudy: no visible global function definition for 'sd'
toSnageeFormat: no visible global function definition for 'is'
toSnageeFormat: no visible global function definition for 'annotation'
toSnageeFormat: no visible global function definition for 'exprs'
toSnageeFormat: no visible global function definition for
  'selectMethod'
toSnageeFormat: no visible global function definition for 'medpolish'
Undefined global functions or variables:
  annotation cor exprs is mad mclapply median medpolish sd selectMethod
Consider adding
  importFrom("methods", "is", "selectMethod")
  importFrom("stats", "cor", "mad", "median", "medpolish", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) qualStudy.Rd:35: Lost braces
    35 | \seealso{\link{SNAGEE}, \link{qualSample}, link{toSnageeFormat}
       |                                                ^
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
SNAGEE-package 9.21   4.55   13.79
qualSample     7.87   4.58   12.46
* 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/SNAGEE.Rcheck/00check.log'
for details.


Installation output

SNAGEE.Rcheck/00install.out

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


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'SNAGEE' ...
** using staged installation
** R
** 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 (SNAGEE)

Tests output


Example timings

SNAGEE.Rcheck/SNAGEE-Ex.timings

nameusersystemelapsed
SNAGEE-package 9.21 4.5513.79
qualSample 7.87 4.5812.46
qualStudy1.330.111.45
toSnageeFormat1.320.111.44