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This page was generated on 2022-01-14 13:07:04 -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 RNAsense on tokay2


To the developers/maintainers of the RNAsense package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAsense.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 1634/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAsense 1.8.0  (landing page)
Marcus Rosenblatt
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/RNAsense
git_branch: RELEASE_3_14
git_last_commit: 9f8a50b
git_last_commit_date: 2021-10-26 12:55:58 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RNAsense
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAsense.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RNAsense_1.8.0.tar.gz
StartedAt: 2022-01-14 01:20:22 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 01:47:19 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 1616.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RNAsense.Rcheck
Warnings: 1

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:RNAsense.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RNAsense_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RNAsense.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 'RNAsense/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAsense' version '1.8.0'
* 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 whether package 'RNAsense' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
combineResults: no visible binding for global variable 'resultSwitch'
combineResults: no visible binding for global variable 'resultFC'
combineResults : getFCupdown: no visible binding for global variable
  'resultFC'
combineResults : getFCupdown: no visible binding for global variable
  'name'
combineResults : getFCupdown: no visible binding for global variable
  'FCdetect'
getFC: no visible binding for global variable 'mydata'
getFC: no visible binding for global variable 'analyzeConditions'
getFC: no visible binding for global variable 'times'
getSwitch: no visible binding for global variable 'mydata'
getSwitch: no visible binding for global variable 'times'
outputGeneTables: no visible binding for global variable
  'resultCombined'
outputGeneTables: no visible binding for global variable 'times'
outputGeneTables: no visible binding for global variable
  'analyzeConditions'
outputGeneTables: no visible binding for global variable 'timepoint'
outputGeneTables: no visible binding for global variable 'FCdown'
outputGeneTables: no visible binding for global variable 'FCup'
outputGeneTables: no visible binding for global variable 'experiment'
plotSSGS: no visible binding for global variable 'resultCombined'
plotSSGS: no visible binding for global variable 'times'
plotSSGS: no visible binding for global variable 'analyzeConditions'
plotSSGS : getFT: no visible binding for global variable 'result'
plotSSGS : getFT: no visible binding for global variable 'timepoint'
plotSSGS : getFT: no visible binding for global variable 'FCdown'
plotSSGS : getFT: no visible binding for global variable 'FCup'
plotSSGS : <anonymous> : <anonymous> : <anonymous> : <anonymous>: no
  visible binding for global variable 'experiment'
plotSSGS: no visible binding for global variable 'xaxis'
plotSSGS: no visible binding for global variable 'cluster'
Undefined global functions or variables:
  FCdetect FCdown FCup analyzeConditions cluster experiment mydata name
  result resultCombined resultFC resultSwitch timepoint times xaxis
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getFC.Rd':
  'DataFrame'

Missing link or links in documentation object 'getSwitch.Rd':
  'DataFrame'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotSSGS         188.79   0.34  189.22
combineResults   187.15   0.90  188.13
outputGeneTables 186.47   0.36  186.92
getSwitch         97.10   0.13   97.28
getFC             67.77   0.14   67.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
outputGeneTables 178.11   0.02  178.16
combineResults   176.48   0.36  176.91
plotSSGS         170.79   0.06  170.86
getSwitch         98.22   0.08   98.34
getFC             62.38   0.11   62.50
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RNAsense.Rcheck/00check.log'
for details.



Installation output

RNAsense.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/RNAsense_1.8.0.tar.gz && rm -rf RNAsense.buildbin-libdir && mkdir RNAsense.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAsense.buildbin-libdir RNAsense_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RNAsense_1.8.0.zip && rm RNAsense_1.8.0.tar.gz RNAsense_1.8.0.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
 54  815k   54  444k    0     0  1901k      0 --:--:-- --:--:-- --:--:-- 1898k
100  815k  100  815k    0     0  2611k      0 --:--:-- --:--:-- --:--:-- 2614k

install for i386

* installing *source* package 'RNAsense' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RNAsense'
    finding HTML links ... done
    MZsox                                   html  
    finding level-2 HTML links ... done

    combineResults                          html  
    getFC                                   html  
    getSwitch                               html  
    outputGeneTables                        html  
    plotSSGS                                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 'RNAsense' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAsense' as RNAsense_1.8.0.zip
* DONE (RNAsense)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RNAsense' successfully unpacked and MD5 sums checked

Tests output


Example timings

RNAsense.Rcheck/examples_i386/RNAsense-Ex.timings

nameusersystemelapsed
combineResults187.15 0.90188.13
getFC67.77 0.1467.91
getSwitch97.10 0.1397.28
outputGeneTables186.47 0.36186.92
plotSSGS188.79 0.34189.22

RNAsense.Rcheck/examples_x64/RNAsense-Ex.timings

nameusersystemelapsed
combineResults176.48 0.36176.91
getFC62.38 0.1162.50
getSwitch98.22 0.0898.34
outputGeneTables178.11 0.02178.16
plotSSGS170.79 0.06170.86