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This page was generated on 2022-01-26 13:06:36 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 frma on tokay2


To the developers/maintainers of the frma package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/frma.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 686/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frma 1.46.0  (landing page)
Matthew N. McCall
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/frma
git_branch: RELEASE_3_14
git_last_commit: c00c4df
git_last_commit_date: 2021-10-26 11:55:11 -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: frma
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:frma.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings frma_1.46.0.tar.gz
StartedAt: 2022-01-25 19:52:00 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 20:02:53 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 653.2 seconds
RetCode: 0
Status:   OK  
CheckDir: frma.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:frma.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings frma_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/frma.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 'frma/DESCRIPTION' ... OK
* this is package 'frma' version '1.46.0'
* 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 'frma' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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
GNUSE: no visible binding for global variable 'median'
GNUSE: no visible binding for global variable 'quantile'
GNUSE: no visible global function definition for 'boxplot'
barcode: no visible global function definition for 'pnorm'
batchFit: no visible global function definition for 'median'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot<-'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot'
randomeffects<-,frmaExpressionSet: no visible global function
  definition for 'validObject'
residuals<-,frmaExpressionSet: no visible global function definition
  for 'validObject'
se.exprs<-,ExpressionSet: no visible global function definition for
  'validObject'
se.exprs<-,frmaExpressionSet: no visible global function definition for
  'validObject'
weights<-,frmaExpressionSet: no visible global function definition for
  'validObject'
Undefined global functions or variables:
  boxplot median pnorm quantile slot slot<- validObject
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("methods", "slot", "slot<-", "validObject")
  importFrom("stats", "median", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
GNUSE   14.33   0.68   86.62
barcode  9.88   0.71   15.34
frma     8.17   0.15    8.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
GNUSE   14.58   0.27   16.83
frma    10.08   0.08   10.15
barcode  9.08   0.12    9.20
* 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/frma.Rcheck/00check.log'
for details.



Installation output

frma.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/frma_1.46.0.tar.gz && rm -rf frma.buildbin-libdir && mkdir frma.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=frma.buildbin-libdir frma_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL frma_1.46.0.zip && rm frma_1.46.0.tar.gz frma_1.46.0.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 15532  100 15532    0     0   132k      0 --:--:-- --:--:-- --:--:--  133k

install for i386

* installing *source* package 'frma' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'frma'
    finding HTML links ... done
    GNUSE                                   html  
    barcode                                 html  
    frma                                    html  
    frmaExpressionSet-class                 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 'frma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'frma' as frma_1.46.0.zip
* DONE (frma)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'frma' successfully unpacked and MD5 sums checked

Tests output


Example timings

frma.Rcheck/examples_i386/frma-Ex.timings

nameusersystemelapsed
GNUSE14.33 0.6886.62
barcode 9.88 0.7115.34
frma8.170.158.31
frmaExpressionSet-class0.080.000.08

frma.Rcheck/examples_x64/frma-Ex.timings

nameusersystemelapsed
GNUSE14.58 0.2716.83
barcode9.080.129.20
frma10.08 0.0810.15
frmaExpressionSet-class0.090.000.09