James Bullard
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Genominator |
| Branch: RELEASE_3_10 |
| Last Commit: 475c8da |
| Last Changed Date: 2019-10-29 13:08:11 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:19:03 -0400 (Wed, 15 Apr 2020).
| Package 688/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Genominator 1.40.0 James Bullard
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Genominator |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Genominator.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Genominator_1.40.0.tar.gz |
| StartedAt: 2020-04-15 03:28:08 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:32:54 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 286.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Genominator.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Genominator.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Genominator_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' 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 ... OK
* checking for portable file names ... OK
* checking whether package 'Genominator' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck/00install.out' for details.
* 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' calls to packages already attached by Depends:
'GenomeGraphs' 'IRanges'
Please remove these calls from your code.
'library' or 'require' call to 'ShortRead' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'GenomeGraphs' 'RSQLite'
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 ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.genominator.coverage plot.genominator.goodness.of.fit
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addPrimingWeights: no visible global function definition for
'varLabels'
addPrimingWeights: no visible global function definition for
'alignData'
addPrimingWeights: no visible global function definition for 'subseq'
addPrimingWeights: no visible global function definition for 'sread'
addPrimingWeights: no visible global function definition for
'AlignedDataFrame'
addPrimingWeights: no visible global function definition for 'pData'
addPrimingWeights: no visible global function definition for
'varMetadata'
computePrimingWeights: no visible global function definition for
'mkAllStrings'
computePrimingWeights : p.compute: no visible global function
definition for 'tables'
computePrimingWeights : p.compute: no visible global function
definition for 'subseq'
computePrimingWeights : p.compute: no visible global function
definition for 'sread'
importFromAlignedReads : weights.AlignedRead: no visible global
function definition for 'varLabels'
importFromAlignedReads : weights.AlignedRead: no visible global
function definition for 'alignData'
importFromAlignedReads : importObject: no visible global function
definition for 'position'
importFromAlignedReads : importObject: no visible global function
definition for 'chromosome'
importFromAlignedReads : importObject: no visible global function
definition for 'varLabels'
importFromAlignedReads : importObject: no visible global function
definition for 'alignData'
importFromAlignedReads: no visible global function definition for
'readAligned'
makeAnnoFactory: no visible global function definition for
'DisplayPars'
makeAnnoFactory : regionAnno.Biomart: no visible global function
definition for 'geneRegionBiomart'
makeAnnoFactory : regionAnno.AnnoData: no visible global function
definition for 'makeAnnotationTrack'
makeRegionPlotter : <anonymous>: no visible global function definition
for 'DisplayPars'
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
function definition for 'makeBaseTrack'
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
function definition for 'makeGenericArray'
makeRegionPlotter : <anonymous>: no visible global function definition
for 'makeGenomeAxis'
makeRegionPlotter : <anonymous>: no visible global function definition
for 'gdPlot'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
function definition for 'qchisq'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
function definition for 'ppoints'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
function definition for 'qunif'
plot.genominator.goodness.of.fit : <anonymous>: no visible global
function definition for 'qqplot'
Undefined global functions or variables:
AlignedDataFrame DisplayPars alignData chromosome gdPlot
geneRegionBiomart makeAnnotationTrack makeBaseTrack makeGenericArray
makeGenomeAxis mkAllStrings pData position ppoints qchisq qqplot
qunif readAligned sread subseq tables varLabels varMetadata
Consider adding
importFrom("stats", "ppoints", "qchisq", "qqplot", "qunif")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'ExpData,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 or elapsed time > 5s
user system elapsed
joinExpData 13.94 0.03 14.00
addPrimingWeights 7.92 1.12 9.11
plot.genominator.coverage 6.97 0.03 7.00
aggregateExpData 5.31 0.02 5.34
computeCoverage 2.20 0.07 5.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
joinExpData 13.61 0.04 16.88
addPrimingWeights 8.42 0.72 9.17
plot.genominator.coverage 7.39 0.05 7.63
aggregateExpData 5.75 0.01 5.89
collapseExpData 5.11 0.02 5.13
* 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 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck/00check.log'
for details.
Genominator.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Genominator_1.40.0.tar.gz && rm -rf Genominator.buildbin-libdir && mkdir Genominator.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Genominator.buildbin-libdir Genominator_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Genominator_1.40.0.zip && rm Genominator_1.40.0.tar.gz Genominator_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 1478k 100 1478k 0 0 24.4M 0 --:--:-- --:--:-- --:--:-- 26.2M
install for i386
* installing *source* package 'Genominator' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'GenomeGraphs' is deprecated and will be removed from
Bioconductor version 3.11
** help
*** installing help indices
converting help for package 'Genominator'
finding HTML links ... done
ExpData html
Genominator html
addPrimingWeights html
aggregateExpData html
applyMapped html
collapseExpData html
computeCoverage html
computePrimingWeights html
getRegion html
importFromAlignedReads html
importToExpData html
joinExpData html
makeGeneRepresentation html
mergeWithAnnotation html
plot.genominator.coverage html
plot.genominator.goodness.of.fit html
regionGoodnessOfFit-methods html
splitByAnnotation html
summarizeByAnnotation html
summarizeExpData html
validAnnotation html
yeastAnno html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
Bioconductor version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Genominator' ...
** testing if installed package can be loaded
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
Bioconductor version 3.11
* MD5 sums
packaged installation of 'Genominator' as Genominator_1.40.0.zip
* DONE (Genominator)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Genominator' successfully unpacked and MD5 sums checked
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Genominator.Rcheck/examples_i386/Genominator-Ex.timings
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Genominator.Rcheck/examples_x64/Genominator-Ex.timings
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