JunctionSeq 1.6.0
Stephen Hartley
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/JunctionSeq | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && mkdir JunctionSeq.buildbin-libdir JunctionSeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=JunctionSeq.buildbin-libdir JunctionSeq_1.6.0.tar.gz >JunctionSeq.Rcheck\00install.out 2>&1 && cp JunctionSeq.Rcheck\00install.out JunctionSeq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=JunctionSeq.buildbin-libdir --install="check:JunctionSeq-install.out" --force-multiarch --no-vignettes --timings JunctionSeq_1.6.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/JunctionSeq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'JunctionSeq/DESCRIPTION' ... OK
* this is package 'JunctionSeq' version '1.6.0'
* 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 'JunctionSeq' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("DESeq2_fitBeta", ..., PACKAGE = "DESeq2")
.Call("DESeq2_fitDisp", ..., PACKAGE = "DESeq2")
.Call("DESeq2_fitDispGrid", ..., PACKAGE = "DESeq2")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
testFeatureForDJU.fromRow.simpleNormDist: no visible global function
definition for 'glm.fit'
Undefined global functions or variables:
glm.fit
Consider adding
importFrom("stats", "glm.fit")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
buildAllPlots 11.99 58.65 71.25
buildAllPlotsForGene 1.25 6.10 7.39
defaultColorList 1.38 5.00 6.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
buildAllPlots 13.61 61.63 75.88
defaultColorList 1.49 5.29 11.18
buildAllPlotsForGene 1.11 5.66 6.78
estimateEffectSizes 3.78 0.02 8.57
* 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-3.5-bioc/meat/JunctionSeq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'JunctionSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'JunctionSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'JunctionSeq' as JunctionSeq_1.6.0.zip
* DONE (JunctionSeq)