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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1800/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
safe 3.45.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/safe
git_branch: devel
git_last_commit: 0dddf91
git_last_commit_date: 2024-04-30 10:13:45 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for safe on palomino6

To the developers/maintainers of the safe package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/safe.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: safe
Version: 3.45.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings safe_3.45.0.tar.gz
StartedAt: 2024-07-16 03:36:25 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 03:38:13 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 108.1 seconds
RetCode: 0
Status:   OK  
CheckDir: safe.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings safe_3.45.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/safe.Rcheck'
* using R version 4.4.1 (2024-06-14 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 'safe/DESCRIPTION' ... OK
* this is package 'safe' version '3.45.0'
* 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 'safe' 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 'SparseM' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'GO.db' 'GOstats' 'PFAM.db' 'Rgraphviz' 'doRNG' 'foreach'
  'reactome.db' 'survival'
  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
getCOXresiduals: no visible global function definition for 'Surv'
getCOXresiduals: no visible global function definition for 'coxph'
getCOXresiduals: no visible global function definition for 'residuals'
getCmatrix: no visible binding for global variable 'GOTERM'
safe: no visible binding for global variable 'reactomeEXTID2PATHID'
safe: no visible global function definition for 'safe.express'
safe: no visible global function definition for 'getDoParWorkers'
safe: no visible global function definition for '%dorng%'
safe: no visible global function definition for 'foreach'
safe.toptable: no visible binding for global variable 'GOTERM'
safe.toptable: no visible binding for global variable 'PFAMSCOP'
safe.toptable: no visible binding for global variable 'reactome.db'
safedag: no visible binding for global variable 'GOTERM'
safedag: no visible global function definition for 'GOGraph'
safedag: no visible global function definition for 'makeNodeAttrs'
safedag: no visible global function definition for 'subGraph'
safedag: no visible global function definition for 'agopen'
safeplot: no visible binding for global variable 'GOTERM'
safeplot: no visible binding for global variable 'PFAMID'
Undefined global functions or variables:
  %dorng% GOGraph GOTERM PFAMID PFAMSCOP Surv agopen coxph foreach
  getDoParWorkers makeNodeAttrs reactome.db reactomeEXTID2PATHID
  residuals safe.express subGraph
Consider adding
  importFrom("stats", "residuals")
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' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'SAFEmanual3.pdf' from 811Kb to 377Kb
  consider running tools::compactPDF() on these files,
  or build the source package with --compact-vignettes
* checking files in 'vignettes' ... OK
* checking examples ... 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/safe.Rcheck/00check.log'
for details.


Installation output

safe.Rcheck/00install.out

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL safe
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'safe' ...
** 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 (safe)

Tests output


Example timings

safe.Rcheck/safe-Ex.timings

nameusersystemelapsed
getCmatrix000
safe0.140.060.20
safeplot0.080.040.11