Matthew N. McCall
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/frmaTools |
| Branch: RELEASE_3_9 |
| Last Commit: 6a87073 |
| Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:52 -0400 (Wed, 16 Oct 2019).
| Package 593/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| frmaTools 1.36.0 Matthew N. McCall
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: frmaTools |
| Version: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:frmaTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings frmaTools_1.36.0.tar.gz |
| StartedAt: 2019-10-16 02:55:10 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:56:12 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 61.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: frmaTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:frmaTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings frmaTools_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/frmaTools.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘frmaTools/DESCRIPTION’ ... OK
* this is package ‘frmaTools’ version ‘1.36.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
convertPlatform 9.682 0.571 10.273
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/frmaTools.Rcheck/00check.log’
for details.
frmaTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL frmaTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘frmaTools’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (frmaTools)
frmaTools.Rcheck/frmaTools-Ex.timings
| name | user | system | elapsed | |
| convertPlatform | 9.682 | 0.571 | 10.273 | |
| makeVectorPackage | 0 | 0 | 0 | |