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CHECK report for frmaTools on tokay2

This page was generated on 2020-10-17 11:56:37 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE frmaTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 642/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frmaTools 1.40.0
Matthew N. McCall
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/frmaTools
Branch: RELEASE_3_11
Last Commit: be745b3
Last Changed Date: 2020-04-27 14:20:56 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: frmaTools
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:frmaTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings frmaTools_1.40.0.tar.gz
StartedAt: 2020-10-17 04:11:31 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:12:38 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 67.1 seconds
RetCode: 0
Status:  OK  
CheckDir: frmaTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:frmaTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings frmaTools_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/frmaTools.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'frmaTools/DESCRIPTION' ... OK
* this is package 'frmaTools' version '1.40.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/VectorPkg-template/data/.dummy.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'frmaTools' 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 'oligo' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'affy'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertPlatform: no visible global function definition for
  'cleancdfname'
convertPlatform: no visible global function definition for 'cdfName'
convertPlatform: no visible global function definition for 'probeNames'
convertPlatform: no visible global function definition for 'pmindex'
getFidMetaProbesetCore: no visible global function definition for 'db'
getFidMetaProbesetExtended: no visible global function definition for
  'db'
getFidMetaProbesetFull: no visible global function definition for 'db'
getFidProbeset: no visible global function definition for 'db'
makeMaps: no visible global function definition for 'xy2indices'
makeVectorsAffyBatch: no visible global function definition for
  'ReadAffy'
makeVectorsAffyBatch: no visible global function definition for
  'bg.correct.rma'
makeVectorsAffyBatch: no visible global function definition for 'pm'
makeVectorsAffyBatch: no visible global function definition for
  'probeNames'
makeVectorsAffyBatch: no visible global function definition for
  'pmindex'
makeVectorsAffyBatch: no visible global function definition for
  'packageVersion'
makeVectorsFeatureSet: no visible global function definition for
  'read.celfiles'
makeVectorsFeatureSet: no visible global function definition for
  'backgroundCorrect'
Undefined global functions or variables:
  ReadAffy backgroundCorrect bg.correct.rma cdfName cleancdfname db
  packageVersion pm pmindex probeNames read.celfiles xy2indices
Consider adding
  importFrom("utils", "packageVersion")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
convertPlatform 8.36   0.39    9.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
convertPlatform  6.4   0.22    6.62
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/frmaTools.Rcheck/00check.log'
for details.



Installation output

frmaTools.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/frmaTools_1.40.0.tar.gz && rm -rf frmaTools.buildbin-libdir && mkdir frmaTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=frmaTools.buildbin-libdir frmaTools_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL frmaTools_1.40.0.zip && rm frmaTools_1.40.0.tar.gz frmaTools_1.40.0.zip
###
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  % 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  7404  100  7404    0     0   117k      0 --:--:-- --:--:-- --:--:--  131k

install for i386

* installing *source* package 'frmaTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'frmaTools'
    finding HTML links ... done
    convertPlatform                         html  
    makeVectorPackage                       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 'frmaTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'frmaTools' as frmaTools_1.40.0.zip
* DONE (frmaTools)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'frmaTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

frmaTools.Rcheck/examples_i386/frmaTools-Ex.timings

nameusersystemelapsed
convertPlatform8.360.399.56
makeVectorPackage000

frmaTools.Rcheck/examples_x64/frmaTools-Ex.timings

nameusersystemelapsed
convertPlatform6.400.226.62
makeVectorPackage000