synapter 1.15.2
Laurent Gatto and Sebastian Gibb
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter | | Last Changed Rev: 117512 / Revision: 121152 | | Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf synapter.buildbin-libdir synapter.Rcheck && mkdir synapter.buildbin-libdir synapter.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=synapter.buildbin-libdir synapter_1.15.2.tar.gz >synapter.Rcheck\00install.out 2>&1 && cp synapter.Rcheck\00install.out synapter-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=synapter.buildbin-libdir --install="check:synapter-install.out" --force-multiarch --no-vignettes --timings synapter_1.15.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/synapter.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 'synapter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'synapter' version '1.15.2'
* 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 'synapter' 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
calculateGridPerformance: no visible global function definition for
'setNames'
doHDMSePredictions: no visible global function definition for 'predict'
getQs: no visible global function definition for 'quantile'
makeMaster : <anonymous>: no visible global function definition for
'loess'
makeMaster : <anonymous>: no visible global function definition for
'predict'
modelRetTime: no visible global function definition for 'loess'
modelRetTime: no visible global function definition for 'predict'
modelRetTime: no visible global function definition for 'fitted'
plot.all.features: no visible global function definition for 'par'
plot.all.features: no visible global function definition for 'grid'
plot.some.features: no visible global function definition for 'text'
plot.some.features: no visible global function definition for 'grid'
plot.some.features: no visible global function definition for 'points'
plot.some.features: no visible global function definition for 'predict'
plot.some.features: no visible global function definition for 'rect'
plot.some.features: no visible global function definition for 'legend'
plotErrorPpm: no visible global function definition for 'layout'
plotErrorPpm: no visible global function definition for 'par'
plotErrorPpm: no visible global function definition for 'hist'
plotErrorPpm: no visible global function definition for 'rug'
plotErrorPpm: no visible global function definition for 'legend'
plotErrorPpm: no visible global function definition for 'lines'
plotErrorPpm: no visible global function definition for 'density'
plotErrorPpm: no visible global function definition for 'rnorm'
plotErrorPpm: no visible global function definition for 'sd'
plotErrorPpm: no visible global function definition for 'abline'
plotErrorPpm: no visible global function definition for 'quantile'
plotErrorPpm: no visible global function definition for 'boxplot'
plotLowess: no visible global function definition for 'par'
plotLowess: no visible global function definition for 'abline'
plotLowess: no visible global function definition for 'grid'
plotLowess: no visible global function definition for 'lowess'
plotLowess : <anonymous>: no visible global function definition for
'lowess'
plotLowess : <anonymous>: no visible global function definition for
'lines'
plotLowess: no visible global function definition for 'legend'
plotLowess2: no visible global function definition for 'grid'
plotLowess2: no visible global function definition for 'polygon'
plotLowess2: no visible global function definition for 'abline'
plotLowess2: no visible global function definition for 'points'
plotLowess2: no visible global function definition for 'lines'
plotLowess2: no visible global function definition for 'fitted'
plotRetTimeDiffs: no visible global function definition for 'fitted'
plotRetTimeDiffs: no visible global function definition for 'hist'
plotRetTimeDiffs: no visible global function definition for 'rug'
qPlot: no visible global function definition for 'axis'
qPlot: no visible global function definition for 'grid'
qPlot: no visible global function definition for 'abline'
qPlot: no visible global function definition for 'segments'
synergise: no visible global function definition for 'tk_choose.dir'
synergise: no visible global function definition for 'jpeg'
synergise: no visible global function definition for 'dev.off'
synergise: no visible global function definition for 'svg'
plot,MasterFdrResults-missing: no visible global function definition
for 'text'
plot,MasterFdrResults-missing: no visible global function definition
for 'abline'
plot,MasterFdrResults-missing: no visible global function definition
for 'points'
plotFdr,Synapter : .qplot: no visible global function definition for
'quantile'
plotFdr,Synapter : .qplot: no visible global function definition for
'lines'
plotFdr,Synapter : .qplot: no visible global function definition for
'legend'
plotFdr,Synapter: no visible global function definition for 'par'
plotPpmError,Synapter: no visible global function definition for 'par'
Undefined global functions or variables:
abline axis boxplot density dev.off fitted grid hist jpeg layout
legend lines loess lowess par points polygon predict quantile rect
rnorm rug sd segments setNames svg text tk_choose.dir
Consider adding
importFrom("grDevices", "dev.off", "jpeg", "svg")
importFrom("graphics", "abline", "axis", "boxplot", "grid", "hist",
"layout", "legend", "lines", "par", "points", "polygon",
"rect", "rug", "segments", "text")
importFrom("stats", "density", "fitted", "loess", "lowess", "predict",
"quantile", "rnorm", "sd", "setNames")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
Synapter 6.87 0.08 6.97
synergise 5.49 0.78 6.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Synapter 7.18 0.14 9.46
synergise 6.00 0.82 7.54
* 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 NOTE
See
'D:/biocbld/bbs-3.4-bioc/meat/synapter.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'synapter' ...
** R
** data
** 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 'synapter' ...
** 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 'synapter' as synapter_1.15.2.zip
* DONE (synapter)