Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:07:06 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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

CHECK results for safe on tokay2


To the developers/maintainers of the safe package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1686/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
safe 3.34.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/safe
git_branch: RELEASE_3_14
git_last_commit: 527fe92
git_last_commit_date: 2021-10-26 11:47:48 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: safe
Version: 3.34.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings safe_3.34.0.tar.gz
StartedAt: 2022-01-14 01:36:08 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 01:38:18 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 130.3 seconds
RetCode: 0
Status:   OK  
CheckDir: safe.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings safe_3.34.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/safe.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'safe/DESCRIPTION' ... OK
* this is package 'safe' version '3.34.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/safe.Rcheck/00check.log'
for details.



Installation output

safe.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/safe_3.34.0.tar.gz && rm -rf safe.buildbin-libdir && mkdir safe.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=safe.buildbin-libdir safe_3.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL safe_3.34.0.zip && rm safe_3.34.0.tar.gz safe_3.34.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7  164k    7 12027    0     0   6068      0  0:00:27  0:00:01  0:00:26  6068
100  164k  100  164k    0     0  82638      0  0:00:02  0:00:02 --:--:-- 82686

install for i386

* installing *source* package 'safe' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'safe'
    finding HTML links ... done
    SAFE-class                              html  
    gene.results                            html  
    getCmatrix                              html  
    p53.stat                                html  
    safe-internal                           html  
    safe-package                            html  
    safe                                    html  
    safe.toptable                           html  
    safedag                                 html  
    safeplot                                html  
** 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

install for x64

* installing *source* package 'safe' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'safe' as safe_3.34.0.zip
* DONE (safe)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'safe' successfully unpacked and MD5 sums checked

Tests output


Example timings

safe.Rcheck/examples_i386/safe-Ex.timings

nameusersystemelapsed
getCmatrix000
safe0.140.020.16
safeplot0.160.000.15

safe.Rcheck/examples_x64/safe-Ex.timings

nameusersystemelapsed
getCmatrix000
safe0.170.030.20
safeplot0.110.000.11