Risa 1.15.0
Alejandra Gonzalez-Beltran
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Risa | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf Risa.buildbin-libdir Risa.Rcheck && mkdir Risa.buildbin-libdir Risa.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Risa.buildbin-libdir Risa_1.15.0.tar.gz >Risa.Rcheck\00install.out 2>&1 && cp Risa.Rcheck\00install.out Risa-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Risa.buildbin-libdir --install="check:Risa-install.out" --force-multiarch --no-vignettes --timings Risa_1.15.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Risa.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 'Risa/DESCRIPTION' ... OK
* this is package 'Risa' version '1.15.0'
* 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 'Risa' 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 ... OK
* checking R code for possible problems ... NOTE
getPackagesInBiocView: no visible global function definition for 'data'
readISAtabZip: no visible global function definition for 'unzip'
suggestBiocPackage: no visible global function definition for
'read.csv'
write.assay.file: no visible global function definition for
'write.table'
write.investigation.file: no visible global function definition for
'write.table'
write.study.file: no visible global function definition for
'write.table'
initialize,ISATab: no visible global function definition for
'count.fields'
initialize,ISATab: no visible global function definition for
'read.table'
initialize,ISATab : <anonymous>: no visible global function definition
for 'read.table'
initialize,ISATab : <anonymous> : <anonymous>: no visible global
function definition for 'read.table'
initialize,ISATab: no visible global function definition for 'na.omit'
Undefined global functions or variables:
count.fields data na.omit read.csv read.table unzip write.table
Consider adding
importFrom("stats", "na.omit")
importFrom("utils", "count.fields", "data", "read.csv", "read.table",
"unzip", "write.table")
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 'AssayTab,ANY,ANY,ANY'
generic '[' and siglist 'ISATab,ANY,ANY,ANY'
generic '[<-' and siglist 'AssayTab,ANY,ANY,ANY'
generic '[<-' and siglist 'ISATab,ANY,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 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
Risa-package 0.19 0.08 13.42
processAssayXcmsSet.1factor 0.13 0.00 14.81
processAssayXcmsSet 0.03 0.02 15.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
processAssayXcmsSet.1factor 0.10 0.02 19.66
processAssayXcmsSet 0.06 0.01 18.94
* 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: 1 WARNING, 1 NOTE
See
'D:/biocbld/bbs-3.4-bioc/meat/Risa.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Risa' ...
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
install for x64
* installing *source* package 'Risa' ...
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
* MD5 sums
packaged installation of 'Risa' as Risa_1.15.0.zip
* DONE (Risa)