JunctionSeq 1.3.4
Stephen Hartley
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/JunctionSeq | | Last Changed Rev: 117778 / Revision: 121152 | | Last Changed Date: 2016-05-23 10:31:32 -0700 (Mon, 23 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=JunctionSeq.buildbin-libdir JunctionSeq_1.3.4.tar.gz >JunctionSeq.Rcheck\00install.out 2>&1 && cp JunctionSeq.Rcheck\00install.out JunctionSeq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=JunctionSeq.buildbin-libdir --install="check:JunctionSeq-install.out" --force-multiarch --no-vignettes --timings JunctionSeq_1.3.4.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/JunctionSeq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.3.4'
* 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
* 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 ... NOTE
Foreign function calls to a different package:
.Call("DESeq2_fitBeta", ..., PACKAGE = "DESeq2")
.Call("DESeq2_fitDisp", ..., PACKAGE = "DESeq2")
.Call("DESeq2_fitDispGrid", ..., PACKAGE = "DESeq2")
.Call("DESeq2_rlogGrid", ..., 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 10.53 59.03 72.66
defaultColorList 1.51 6.70 8.22
buildAllPlotsForGene 1.51 6.18 7.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
buildAllPlots 10.64 58.70 71.62
defaultColorList 1.64 6.07 8.87
buildAllPlotsForGene 1.47 6.15 8.26
estimateEffectSizes 4.36 0.01 5.43
* 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
'D:/biocbld/bbs-3.4-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_1.3.4.zip
* DONE (JunctionSeq)