Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:06:00 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 CAFE on tokay2


To the developers/maintainers of the CAFE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAFE.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 234/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAFE 1.30.0  (landing page)
Sander Bollen
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/CAFE
git_branch: RELEASE_3_14
git_last_commit: 95b0e67
git_last_commit_date: 2021-10-26 12:12:15 -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: CAFE
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAFE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CAFE_1.30.0.tar.gz
StartedAt: 2022-01-16 17:52:20 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 17:59:29 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 428.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CAFE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAFE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CAFE_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CAFE.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 'CAFE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CAFE' version '1.30.0'
* 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 'CAFE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... WARNING
'::' or ':::' import not declared from: 'BiocManager'
'loadNamespace' or 'requireNamespace' call not declared from: 'BiocManager'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Armchisqr: no visible global function definition for 'chisq.test'
ArmfisherExact: no visible global function definition for 'fisher.test'
ProcessCels: no visible global function definition for
  'install.packages'
ProcessCels: no visible global function definition for 'download.file'
ProcessCels: no visible global function definition for 'read.table'
ProcessCels: no visible global function definition for 'txtProgressBar'
ProcessCels: no visible global function definition for
  'setTxtProgressBar'
ProcessCels: no visible global function definition for 'na.omit'
allBandsOnChrom: no visible global function definition for
  'fisher.test'
allBandsOnChromChi: no visible global function definition for
  'chisq.test'
armStats: no visible global function definition for 'p.adjust'
bandStats: no visible global function definition for 'p.adjust'
chisqr: no visible global function definition for 'chisq.test'
chromosomeStats: no visible global function definition for 'p.adjust'
discontPlot: no visible global function definition for 'png'
discontPlot: no visible global function definition for 'dev.off'
discontPlot: no visible global function definition for 'data'
facetPlot: no visible global function definition for 'png'
facetPlot: no visible global function definition for 'dev.off'
facetPlot: no visible global function definition for 'na.omit'
fisher.method: no visible global function definition for 'pchisq'
fisherExact: no visible global function definition for 'fisher.test'
makelevels: no visible global function definition for 'na.omit'
rawPlot: no visible global function definition for 'png'
rawPlot: no visible global function definition for 'dev.off'
rawPlot: no visible global function definition for 'data'
slidPlot: no visible global function definition for 'png'
slidPlot: no visible global function definition for 'dev.off'
slidPlot: no visible global function definition for 'data'
Undefined global functions or variables:
  chisq.test data dev.off download.file fisher.test install.packages
  na.omit p.adjust pchisq png read.table setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("stats", "chisq.test", "fisher.test", "na.omit", "p.adjust",
             "pchisq")
  importFrom("utils", "data", "download.file", "install.packages",
             "read.table", "setTxtProgressBar", "txtProgressBar")
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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CAFE.Rcheck/00check.log'
for details.



Installation output

CAFE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CAFE_1.30.0.tar.gz && rm -rf CAFE.buildbin-libdir && mkdir CAFE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAFE.buildbin-libdir CAFE_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CAFE_1.30.0.zip && rm CAFE_1.30.0.tar.gz CAFE_1.30.0.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
100 2276k  100 2276k    0     0  4645k      0 --:--:-- --:--:-- --:--:-- 4655k

install for i386

* installing *source* package 'CAFE' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CAFE'
    finding HTML links ... done
    CAFE-package                            html  
    CAFE                                    html  
    ProcessCels                             html  
    armStats                                html  
    bandStats                               html  
    chromosomeStats                         html  
    cliSubset                               html  
    discontPlot                             html  
    discontSmooth                           html  
    facetPlot                               html  
    fisher.method                           html  
    guiSubset                               html  
    rawPlot                                 html  
    slidPlot                                html  
    slidSmooth                              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 'CAFE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAFE' as CAFE_1.30.0.zip
* DONE (CAFE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CAFE' successfully unpacked and MD5 sums checked

Tests output

CAFE.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #BiocGenerics:::testPackage("CAFE")
> 
> proc.time()
   user  system elapsed 
   0.25    0.07    0.31 

CAFE.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #BiocGenerics:::testPackage("CAFE")
> 
> proc.time()
   user  system elapsed 
   0.28    0.01    0.28 

Example timings

CAFE.Rcheck/examples_i386/CAFE-Ex.timings

nameusersystemelapsed
CAFE-package000
CAFE1.090.131.24
ProcessCels000
armStats2.870.133.40
bandStats1.020.091.11
chromosomeStats101
cliSubset000
discontPlot1.440.131.57
discontSmooth000
facetPlot3.010.423.43
fisher.method000
guiSubset000
rawPlot1.170.111.29
slidPlot1.130.081.20
slidSmooth000

CAFE.Rcheck/examples_x64/CAFE-Ex.timings

nameusersystemelapsed
CAFE-package000
CAFE0.580.010.59
ProcessCels000
armStats1.180.021.20
bandStats2.210.002.20
chromosomeStats0.780.040.83
cliSubset000
discontPlot0.920.050.97
discontSmooth000
facetPlot3.250.443.69
fisher.method000
guiSubset000
rawPlot1.300.081.37
slidPlot1.150.011.18
slidSmooth000